1
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Vishweshwaraiah YL, Hnath B, Wang J, Chandler M, Mukherjee A, Yennawar NH, Booker SJ, Afonin KA, Dokholyan NV. A Piecewise Design Approach to Engineering a Miniature ACE2 Mimic to Bind SARS-CoV-2. ACS Appl Bio Mater 2024. [PMID: 38700999 DOI: 10.1021/acsabm.4c00222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/05/2024]
Abstract
As the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continues its global spread, the exploration of novel therapeutic and diagnostic strategies is still needed. The virus enters host cells by binding the angiotensin-converting enzyme 2 (ACE2) receptor through the spike protein. Here, we develop an engineered, small, stable, and catalytically inactive version of ACE2, termed miniature ACE2 (mACE2), designed to bind the spike protein with high affinity. Employing a magnetic nanoparticle-based assay, we harnessed the strong binding affinity of mACE2 to develop a sensitive and specific platform for the detection or neutralization of SARS-CoV-2. Our findings highlight the potential of engineered mACE2 as a valuable tool in the fight against SARS-CoV-2. The success of developing such a small reagent based on a piecewise molecular design serves as a proof-of-concept approach for the rapid deployment of such agents to diagnose and fight other viral diseases.
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Affiliation(s)
| | - Brianna Hnath
- Department of Pharmacology, Penn State College of Medicine, Hershey, Pennsylvania 17033-0850, United States
- Department of Biomedical Engineering, Penn State University, University Park, Pennsylvania 16802, United States
| | - Jian Wang
- Department of Pharmacology, Penn State College of Medicine, Hershey, Pennsylvania 17033-0850, United States
| | - Morgan Chandler
- Department of Chemistry, University of North Carolina at Charlotte, Charlotte, North Carolina 28223, United States
| | - Arnab Mukherjee
- Department of Chemistry, Penn State University, University Park, Pennsylvania 16802, United States
- The Howard Hughes Medical Institute, Penn State University, University Park, Pennsylvania 16802, United States
| | - Neela H Yennawar
- The Huck Institutes of the Life Sciences, Penn State University, University Park, Pennsylvania 16802, United States
| | - Squire J Booker
- Department of Chemistry, Penn State University, University Park, Pennsylvania 16802, United States
- The Howard Hughes Medical Institute, Penn State University, University Park, Pennsylvania 16802, United States
- Department of Biochemistry & Molecular Biology, Penn State University, University Park, Pennsylvania 16802, United States
| | - Kirill A Afonin
- Department of Chemistry, University of North Carolina at Charlotte, Charlotte, North Carolina 28223, United States
| | - Nikolay V Dokholyan
- Department of Pharmacology, Penn State College of Medicine, Hershey, Pennsylvania 17033-0850, United States
- Department of Biomedical Engineering, Penn State University, University Park, Pennsylvania 16802, United States
- Department of Chemistry, University of North Carolina at Charlotte, Charlotte, North Carolina 28223, United States
- Department of Biochemistry & Molecular Biology, Penn State College of Medicine, Hershey, Pennsylvania 17033-0850, United States
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2
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Suptela AJ, Radwan Y, Richardson C, Yan S, Afonin KA, Marriott I. cGAS Mediates the Inflammatory Responses of Human Microglial Cells to Genotoxic DNA Damage. Inflammation 2024; 47:822-836. [PMID: 38148453 DOI: 10.1007/s10753-023-01946-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 12/01/2023] [Accepted: 12/07/2023] [Indexed: 12/28/2023]
Abstract
Genomic instability is a key driving force for the development and progression of many age-related neurodegenerative diseases and central nervous system (CNS) cancers. Recently, the cytosolic DNA sensor, cyclic GMP-AMP synthase (cGAS), has been shown to detect and respond to self-DNA accumulation resulting from DNA damaging insults in peripheral cell types. cGAS has been shown to be important in the responses of microglia to DNA viruses and amyloid beta, and we have reported that it underlies the responses of human microglia to exogenous DNA. However, the role of this cytosolic sensor in the detection of self-DNA by glia is poorly understood and its ability to mediate the cellular responses of human microglia to genotoxic DNA damage has not been established. Here, we describe the ability of ionizing radiation and oxidative stress to elicit genomic DNA damage in human microglial cells and to stimulate the production of key inflammatory mediators by these cells in an NF-kB dependent manner. Importantly, we have utilized CRISPR/Cas9 and siRNA-mediated knockdown approaches and a pharmacological inhibitor of the cGAS adaptor protein stimulator of interferon genes (STING) to demonstrate that the cGAS-STING pathway plays a critical role in the generation of these microglial immune responses to such genotoxic insults. Together, these studies support the notion that cGAS mediates the detection of cytosolic self-DNA by microglia, providing a potential mechanism linking genomic instability to the development of CNS cancers and neurodegenerative disorders.
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Affiliation(s)
- Alexander J Suptela
- Department of Biological Sciences, University of North Carolina at Charlotte, 9201 University City Blvd., Charlotte, NC, 28223, USA
| | - Yasmine Radwan
- Department of Chemistry, University of North Carolina at Charlotte, Charlotte, NC, USA
| | - Christine Richardson
- Department of Biological Sciences, University of North Carolina at Charlotte, 9201 University City Blvd., Charlotte, NC, 28223, USA
| | - Shan Yan
- Department of Biological Sciences, University of North Carolina at Charlotte, 9201 University City Blvd., Charlotte, NC, 28223, USA
| | - Kirill A Afonin
- Department of Chemistry, University of North Carolina at Charlotte, Charlotte, NC, USA
| | - Ian Marriott
- Department of Biological Sciences, University of North Carolina at Charlotte, 9201 University City Blvd., Charlotte, NC, 28223, USA.
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3
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Rebolledo LP, Ke W, Cedrone E, Wang J, Majithia K, Johnson MB, Dokholyan NV, Dobrovolskaia MA, Afonin KA. Immunostimulation of Fibrous Nucleic Acid Nanoparticles Can be Modulated through Aptamer-Based Functional Moieties: Unveiling the Structure-Activity Relationship and Mechanistic Insights. ACS Appl Mater Interfaces 2024; 16:8430-8441. [PMID: 38344840 PMCID: PMC10895590 DOI: 10.1021/acsami.3c17779] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Revised: 01/23/2024] [Accepted: 01/30/2024] [Indexed: 02/23/2024]
Abstract
Fibrous nanomaterials containing silica, titanium oxide, and carbon nanotubes are notoriously known for their undesirable inflammatory responses and associated toxicities that have been extensively studied in the environmental and occupational toxicology fields. Biopersistance and inflammation of "hard" nanofibers prevent their broader biomedical applications. To utilize the structural benefits of fibrous nanomaterials for functionalization with moieties of therapeutic significance while preventing undesirable immune responses, researchers employ natural biopolymers─RNA and DNA─to design "soft" and biodegradable nanomaterials with controlled immunorecognition. Nucleic acid nanofibers have been shown to be safe and efficacious in applications that do not require their delivery into the cells such as the regulation of blood coagulation. Previous studies demonstrated that unlike traditional therapeutic nucleic acids (e.g., CpG DNA oligonucleotides) nucleic acid nanoparticles (NANPs), when used without a carrier, are not internalized by the immune cells and, as such, do not induce undesirable cytokine responses. In contrast, intracellular delivery of NANPs results in cytokine responses that are dependent on the physicochemical properties of these nanomaterials. However, the structure-activity relationship of innate immune responses to intracellularly delivered fibrous NANPs is poorly understood. Herein, we employ the intracellular delivery of model RNA/DNA nanofibers functionalized with G-quadruplex-based DNA aptamers to investigate how their structural properties influence cytokine responses. We demonstrate that nanofibers' scaffolds delivered to the immune cells using lipofectamine induce interferon response via the cGAS-STING signaling pathway activation and that DNA aptamers incorporation shields the fibers from recognition by cGAS and results in a lower interferon response. This structure-activity relationship study expands the current knowledge base to inform future practical applications of intracellularly delivered NANPs as vaccine adjuvants and immunotherapies.
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Affiliation(s)
- Laura P Rebolledo
- Nanoscale Science Program, Department of Chemistry, University of North Carolina Charlotte, Charlotte, North Carolina 28223, United States
| | - Weina Ke
- Nanoscale Science Program, Department of Chemistry, University of North Carolina Charlotte, Charlotte, North Carolina 28223, United States
| | - Edward Cedrone
- Nanotechnology Characterization Laboratory, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research Sponsored by the National Cancer Institute, Frederick, Maryland 21701, United States
| | - Jian Wang
- Department of Pharmacology, Penn State College of Medicine, Hershey, Pennsylvania 17033, United States
| | - Krishna Majithia
- Department of Biological Sciences, University of North Carolina Charlotte, Charlotte, North Carolina 28223, United States
| | - M Brittany Johnson
- Department of Biological Sciences, University of North Carolina Charlotte, Charlotte, North Carolina 28223, United States
| | - Nikolay V Dokholyan
- Department of Pharmacology, Penn State College of Medicine, Hershey, Pennsylvania 17033, United States
- Department of Biochemistry & Molecular Biology, Department of Biochemistry & Molecular Biology, Penn State College of Medicine, Hershey, Pennsylvania 17033, United States
| | - Marina A Dobrovolskaia
- Nanotechnology Characterization Laboratory, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research Sponsored by the National Cancer Institute, Frederick, Maryland 21701, United States
| | - Kirill A Afonin
- Nanoscale Science Program, Department of Chemistry, University of North Carolina Charlotte, Charlotte, North Carolina 28223, United States
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4
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Brumett R, Danai L, Coffman A, Radwan Y, Teter M, Hayth H, Doe E, Pranger K, Thornburgh S, Dittmer A, Li Z, Kim TJ, Afonin KA, Khisamutdinov EF. Design and Characterization of Compact, Programmable, Multistranded Nonimmunostimulatory Nucleic Acid Nanoparticles Suitable for Biomedical Applications. Biochemistry 2024; 63:312-325. [PMID: 38271599 DOI: 10.1021/acs.biochem.3c00615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2024]
Abstract
We report a thorough investigation of the role of single-stranded thymidine (ssT) linkers in the stability and flexibility of minimal, multistranded DNA nanostructures. We systematically explore the impact of varying the number of ssTs in three-way junction motifs (3WJs) on their formation and properties. Through various UV melting experiments and molecular dynamics simulations, we demonstrate that while the number of ssTs minimally affects thermodynamic stability, the increasing ssT regions significantly enhance the structural flexibility of 3WJs. Utilizing this knowledge, we design triangular DNA nanoparticles with varying ssTs, all showing exceptional assembly efficiency except for the 0T triangle. All triangles demonstrate enhanced stability in blood serum and are nonimmunostimulatory and nontoxic in mammalian cell lines. The 4T 3WJ is chosen as the building block for constructing other polygons due to its enhanced flexibility and favorable physicochemical characteristics, making it a versatile choice for creating cost-effective, stable, and functional DNA nanostructures that can be stored in the dehydrated forms while retaining their structures. Our study provides valuable insights into the design and application of nucleic acid nanostructures, emphasizing the importance of understanding stability and flexibility in the realm of nucleic acid nanotechnology. Our findings suggest the intricate connection between these ssTs and the structural adaptability of DNA 3WJs, paving the way for more precise design and engineering of nucleic acid nanosystems suitable for broad biomedical applications.
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Affiliation(s)
- Ross Brumett
- Department of Chemistry, Ball State University, Muncie, Indiana 47306, United States
| | - Leyla Danai
- Department of Chemistry, University of North Carolina at Charlotte, Charlotte, North Carolina 28223, United States
| | - Abigail Coffman
- Department of Chemistry, Ball State University, Muncie, Indiana 47306, United States
| | - Yasmine Radwan
- Department of Chemistry, University of North Carolina at Charlotte, Charlotte, North Carolina 28223, United States
| | - Megan Teter
- Department of Chemistry, Ball State University, Muncie, Indiana 47306, United States
| | - Hannah Hayth
- Department of Chemistry, Ball State University, Muncie, Indiana 47306, United States
| | - Erwin Doe
- Department of Chemistry, Ball State University, Muncie, Indiana 47306, United States
| | - Katelynn Pranger
- Department of Chemistry, Ball State University, Muncie, Indiana 47306, United States
| | - Sable Thornburgh
- Department of Chemistry, Ball State University, Muncie, Indiana 47306, United States
| | - Allison Dittmer
- Department of Chemistry, Ball State University, Muncie, Indiana 47306, United States
| | - Zhihai Li
- Department of Chemistry, Ball State University, Muncie, Indiana 47306, United States
| | - Tae Jin Kim
- Department of Physical Sciences, West Virginia University Institute of Technology, Beckley, West Virginia 25801, United States
| | - Kirill A Afonin
- Department of Chemistry, University of North Carolina at Charlotte, Charlotte, North Carolina 28223, United States
| | - Emil F Khisamutdinov
- Department of Chemistry, Ball State University, Muncie, Indiana 47306, United States
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5
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Rolband L, Godakhindi V, Vivero-Escoto JL, Afonin KA. Demonstrating the Synthesis and Antibacterial Properties of Nanostructured Silver. J Chem Educ 2023; 100:3547-3555. [PMID: 37720521 PMCID: PMC10501122 DOI: 10.1021/acs.jchemed.3c00125] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 07/29/2023] [Indexed: 09/19/2023]
Abstract
Investigating and understanding novel antibacterial agents is a necessary task as there is a constant increase in the number of multidrug-resistant bacterial species. The use of nanotechnology to combat drug-resistant bacteria is an important research area. The laboratory experiment described herein demonstrates that changes in the nanostructure of a material lead to significantly different antibacterial efficacies. Silver has been known to be an effective antibacterial agent throughout history, but its therapeutic uses are limited when present as either the bulk material or cations in solution. Silver nanoparticles (AgNPs) and DNA-templated silver nanoclusters (DNA-AgNCs) are both nanostructured silver materials that show vastly different antibacterial activities when incubated with E. coli in liquid culture. This work aims to provide students with hands-on experience in the synthesis and characterization of nanomaterials and basic microbiology skills; moreover, it is applicable to undergraduate and graduate curricula.
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Affiliation(s)
- Lewis Rolband
- Department
of Chemistry, University of North Carolina
at Charlotte, Charlotte, North Carolina 28223, United States
| | - Varsha Godakhindi
- Department
of Chemistry, University of North Carolina
at Charlotte, Charlotte, North Carolina 28223, United States
| | - Juan L. Vivero-Escoto
- Department
of Chemistry, University of North Carolina
at Charlotte, Charlotte, North Carolina 28223, United States
| | - Kirill A. Afonin
- Department
of Chemistry, University of North Carolina
at Charlotte, Charlotte, North Carolina 28223, United States
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6
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Danai L, Ge E, Afonin KA. RNA nanoparticles for targeted therapies of triple-negative breast cancers. Mol Ther Nucleic Acids 2023; 33:885-886. [PMID: 37680990 PMCID: PMC10481346 DOI: 10.1016/j.omtn.2023.08.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/09/2023]
Affiliation(s)
- Leyla Danai
- Nanoscale Science Program, Department of Chemistry, The University of North Carolina at Charlotte, Charlotte, NC 28223, USA
| | - Eva Ge
- Nanoscale Science Program, Department of Chemistry, The University of North Carolina at Charlotte, Charlotte, NC 28223, USA
| | - Kirill A. Afonin
- Nanoscale Science Program, Department of Chemistry, The University of North Carolina at Charlotte, Charlotte, NC 28223, USA
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7
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Afonin KA, Re F, Boraschi D. Editorial: Delivering nucleic acids to immune and non-immune cells. Front Immunol 2023; 14:1237506. [PMID: 37614239 PMCID: PMC10443216 DOI: 10.3389/fimmu.2023.1237506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Accepted: 07/28/2023] [Indexed: 08/25/2023] Open
Affiliation(s)
- Kirill A. Afonin
- Nanoscale Science Program, Department of Chemistry, University of North Carolina Charlotte, Charlotte, NC, United States
| | - Francesca Re
- Department of Medicine and Surgery, University of Milano Bicocca, Milano, Italy
| | - Diana Boraschi
- Shenzhen Institute of Advanced Technology (SIAT) of the Chinese Academy of Science (CAS), and China-Italy Joint Laboratory of Pharmacobiotechnology for Medical Immunomodulation, Shenzhen, China
- Institute of Biochemistry and Cell Biology, Consiglio Nazionale delle Ricerche, Napoli, Italy
- Stazione Zoologica Anton Dohrn, Napoli, Italy
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8
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Gupta AK, Marshall N, Yourston L, Rolband L, Beasock D, Danai L, Skelly E, Afonin KA, Krasnoslobodtsev AV. Optical, structural, and biological properties of silver nanoclusters formed within the loop of a C-12 hairpin sequence. Nanoscale Adv 2023; 5:3500-3511. [PMID: 37383066 PMCID: PMC10295035 DOI: 10.1039/d3na00092c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/12/2023] [Accepted: 06/04/2023] [Indexed: 06/30/2023]
Abstract
Silver nanoclusters (AgNCs) are the next-generation nanomaterials representing supra-atomic structures where silver atoms are organized in a particular geometry. DNA can effectively template and stabilize these novel fluorescent AgNCs. Only a few atoms in size - the properties of nanoclusters can be tuned using only single nucleobase replacement of C-rich templating DNA sequences. A high degree of control over the structure of AgNC could greatly contribute to the ability to fine-tune the properties of silver nanoclusters. In this study, we explore the properties of AgNCs formed on a short DNA sequence with a C12 hairpin loop structure (AgNC@hpC12). We identify three types of cytosines based on their involvement in the stabilization of AgNCs. Computational and experimental results suggest an elongated cluster shape with 10 silver atoms. We found that the properties of the AgNCs depend on the overall structure and relative position of the silver atoms. The emission pattern of the AgNCs depends strongly on the charge distribution, while all silver atoms and some DNA bases are involved in optical transitions based on molecular orbital (MO) visualization. We also characterize the antibacterial properties of silver nanoclusters and propose a possible mechanism of action based on the interactions of AgNCs with molecular oxygen.
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Affiliation(s)
- Akhilesh Kumar Gupta
- Department of Physics, University of Nebraska at Omaha Omaha NE 68182 USA +1402-554-3723
| | - Nolan Marshall
- Department of Physics, University of Nebraska at Omaha Omaha NE 68182 USA +1402-554-3723
| | - Liam Yourston
- Department of Physics, University of Nebraska at Omaha Omaha NE 68182 USA +1402-554-3723
| | - Lewis Rolband
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte Charlotte NC 28223 USA
| | - Damian Beasock
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte Charlotte NC 28223 USA
| | - Leyla Danai
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte Charlotte NC 28223 USA
| | - Elizabeth Skelly
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte Charlotte NC 28223 USA
| | - Kirill A Afonin
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte Charlotte NC 28223 USA
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9
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Dobrovolskaia MA, Afonin KA. Special Issue "Nanotechnology to Overcome the World's Most Critical Health Issues: Liposomes and Beyond-A Themed Issue Dedicated to Professor Yechezkel Barenholz". Molecules 2023; 28:4788. [PMID: 37375343 DOI: 10.3390/molecules28124788] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 06/13/2023] [Indexed: 06/29/2023] Open
Abstract
This Special Issue is intended to celebrate Professor Yechezkel Barenholz's distinguished achievements [...].
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Affiliation(s)
- Marina A Dobrovolskaia
- Nanotechnology Characterization Laboratory, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research Sponsored by the National Cancer Institute, Frederick, MD 21701, USA
| | - Kirill A Afonin
- Nanoscale Science Program, Department of Chemistry, University of North Carolina Charlotte, Charlotte, NC 28223, USA
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10
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Beasock D, Ha A, Halman J, Panigaj M, Wang J, Dokholyan NV, Afonin KA. Break to Build: Isothermal Assembly of Nucleic Acid Nanoparticles (NANPs) via Enzymatic Degradation. Bioconjug Chem 2023. [PMID: 37293781 DOI: 10.1021/acs.bioconjchem.3c00167] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The intrinsic properties of RNA and DNA biopolymers emphasized by engineered nucleic acid nanoparticles (NANPs) offer accelerated development of next-generation therapies. The rational design of NANPs facilitates programmable architectures intended for regulated molecular and cellular interactions. The conventional bottom-up assembly of NANPs relies on the thermal annealing of individual strands. Here, we introduce a concept of nuclease-driven production of NANPs where selective digestion of functionally inert structures leads to isothermal self-assembly of liberated constituents. The working principles, morphological changes, assembly kinetics, and the retention of structural integrity for system components subjected to anhydrous processing and storage are assessed. We show that the assembly of precursors into a single structure improves stoichiometry and enhances the functionality of nuclease-driven products. Furthermore, the experiments with immune reporting cell lines show that the developed protocols retain the immunostimulatory functionality of tested NANPs. The presented approach enables exploitation of the advantages of conditionally produced NANPs and demonstrates that NANPs' stability, immunorecognition, and assembly can be regulated to allow for a more robust functional system.
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Affiliation(s)
- Damian Beasock
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, North Carolina 28223, United States
| | - Anh Ha
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, North Carolina 28223, United States
| | - Justin Halman
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, North Carolina 28223, United States
| | - Martin Panigaj
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, North Carolina 28223, United States
| | - Jian Wang
- Department of Pharmacology, Department of Biochemistry & Molecular Biology, Penn State College of Medicine, Hershey, Pennsylvania 17033, United States
| | - Nikolay V Dokholyan
- Department of Pharmacology, Department of Biochemistry & Molecular Biology, Penn State College of Medicine, Hershey, Pennsylvania 17033, United States
- Department of Biochemistry & Molecular Biology, Department of Biochemistry & Molecular Biology, Penn State College of Medicine, Hershey, Pennsylvania 17033, United States
| | - Kirill A Afonin
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, North Carolina 28223, United States
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11
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Newton HS, Radwan Y, Xu J, Clogston JD, Dobrovolskaia MA, Afonin KA. Change in Lipofectamine Carrier as a Tool to Fine-Tune Immunostimulation of Nucleic Acid Nanoparticles. Molecules 2023; 28:molecules28114484. [PMID: 37298960 DOI: 10.3390/molecules28114484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 05/27/2023] [Accepted: 05/30/2023] [Indexed: 06/12/2023] Open
Abstract
Nucleic acid nanoparticles (NANPs) require a carrier to allow for their intracellular delivery to immune cells. Cytokine production, specifically type I and III interferons, allows for reliable monitoring of the carrier effect on NANP immunostimulation. Recent studies have shown that changes in the delivery platform (e.g., lipid-based carriers vs. dendrimers) can alter NANPs' immunorecognition and downstream cytokine production in various immune cell populations. Herein, we used flow cytometry and measured cytokine induction to show how compositional variations in commercially available lipofectamine carriers impact the immunostimulatory properties of NANPs with different architectural characteristics.
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Affiliation(s)
- Hannah S Newton
- Nanotechnology Characterization Laboratory, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research Sponsored by the National Cancer Institute, Frederick, MD 21701, USA
| | - Yasmine Radwan
- Nanoscale Science Program, Department of Chemistry, University of North Carolina Charlotte, Charlotte, NC 28223, USA
| | - Jie Xu
- Nanotechnology Characterization Laboratory, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research Sponsored by the National Cancer Institute, Frederick, MD 21701, USA
| | - Jeffrey D Clogston
- Nanotechnology Characterization Laboratory, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research Sponsored by the National Cancer Institute, Frederick, MD 21701, USA
| | - Marina A Dobrovolskaia
- Nanotechnology Characterization Laboratory, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research Sponsored by the National Cancer Institute, Frederick, MD 21701, USA
| | - Kirill A Afonin
- Nanoscale Science Program, Department of Chemistry, University of North Carolina Charlotte, Charlotte, NC 28223, USA
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12
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Hartung J, McCann N, Doe E, Hayth H, Benkato K, Johnson MB, Viard M, Afonin KA, Khisamutdinov EF. Toehold-Mediated Shape Transition of Nucleic Acid Nanoparticles. ACS Appl Mater Interfaces 2023. [PMID: 37204867 DOI: 10.1021/acsami.3c01604] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
We introduce a toehold-mediated strand displacement strategy for regulated shape-switching of nucleic acid nanoparticles (NANPs) enabling their sequential transformation from triangular to hexagonal architectures at isothermal conditions. The successful shape transitions were confirmed by electrophoretic mobility shift assays, atomic force microscopy, and dynamic light scattering. Furthermore, implementation of split fluorogenic aptamers allowed for monitoring the individual transitions in real time. Three distinct RNA aptamers─malachite green (MG), broccoli, and mango─were embedded within NANPs as reporter domains to confirm shape transitions. While MG "lights up" within the square, pentagonal, and hexagonal constructs, the broccoli is activated only upon formation of pentagon and hexagon NANPs, and mango reports only the presence of hexagons. Moreover, the designed RNA fluorogenic platform can be employed to construct a logic gate that performs an AND operation with three single-stranded RNA inputs by implementing a non-sequential polygon transformation approach. Importantly, the polygonal scaffolds displayed promising potential as drug delivery agents and biosensors. All polygons exhibited effective cellular internalization followed by specific gene silencing when decorated with fluorophores and RNAi inducers. This work offers a new perspective for the design of toehold-mediated shape-switching nanodevices to activate different light-up aptamers for the development of biosensors, logic gates, and therapeutic devices in the nucleic acid nanotechnology.
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Affiliation(s)
- Jordan Hartung
- Department of Chemistry, Ball State University, Muncie, Indiana 47306, United States
| | - Nathan McCann
- Department of Chemistry, Ball State University, Muncie, Indiana 47306, United States
| | - Erwin Doe
- Department of Chemistry, Ball State University, Muncie, Indiana 47306, United States
| | - Hannah Hayth
- Department of Chemistry, Ball State University, Muncie, Indiana 47306, United States
| | - Kheiria Benkato
- Department of Chemistry, Ball State University, Muncie, Indiana 47306, United States
| | - M Brittany Johnson
- Department of Biology, University of North Carolina at Charlotte, Charlotte, North Carolina 28223, United States
| | - Mathias Viard
- Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland 20892, United States
- Basic Science Program, Leidos Biomedical Research Inc. National Cancer Institute, National Institutes of Health, Frederick, Maryland 21702, United States
| | - Kirill A Afonin
- Department of Chemistry, University of North Carolina at Charlotte, Charlotte, North Carolina 28223, United States
| | - Emil F Khisamutdinov
- Department of Chemistry, Ball State University, Muncie, Indiana 47306, United States
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13
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Danai L, Rolband LA, Perdomo VA, Skelly E, Kim T, Afonin KA. Optical, structural and antibacterial properties of silver nanoparticles and DNA-templated silver nanoclusters. Nanomedicine (Lond) 2023; 18:769-782. [PMID: 37345552 PMCID: PMC10308257 DOI: 10.2217/nnm-2023-0082] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Accepted: 06/06/2023] [Indexed: 06/23/2023] Open
Abstract
Silver nanoparticles (AgNPs) are increasingly considered for biomedical applications as drug-delivery carriers, imaging probes and antibacterial agents. Silver nanoclusters (AgNCs) represent another subclass of nanoscale silver. AgNCs are a promising tool for nanomedicine due to their small size, structural homogeneity, antibacterial activity and fluorescence, which arises from their molecule-like electron configurations. The template-assisted synthesis of AgNCs relies on organic molecules that act as polydentate ligands. In particular, single-stranded nucleic acids reproducibly scaffold AgNCs to provide fluorescent, biocompatible materials that are incorporable in other formulations. This mini review outlines the design and characterization of AgNPs and DNA-templated AgNCs, discusses factors that affect their physicochemical and biological properties, and highlights applications of these materials as antibacterial agents and biosensors.
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Affiliation(s)
- Leyla Danai
- Department of Chemistry, Nanoscale Science Program, The University of North Carolina at Charlotte, Charlotte, NC 28223, USA
| | - Lewis A Rolband
- Department of Chemistry, Nanoscale Science Program, The University of North Carolina at Charlotte, Charlotte, NC 28223, USA
| | | | - Elizabeth Skelly
- Department of Chemistry, Nanoscale Science Program, The University of North Carolina at Charlotte, Charlotte, NC 28223, USA
| | - Taejin Kim
- Physical Sciences Department, West Virginia University Institute of Technology, Beckley, WV 25801, USA
| | - Kirill A Afonin
- Department of Chemistry, Nanoscale Science Program, The University of North Carolina at Charlotte, Charlotte, NC 28223, USA
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14
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Afonin KA, Dokholyan NV. Editorial to "Molecular engineering of biomaterials programmed to operate in living systems". Adv Drug Deliv Rev 2023; 193:114669. [PMID: 36529189 PMCID: PMC10015611 DOI: 10.1016/j.addr.2022.114669] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Kirill A Afonin
- Department of Chemistry, The University of North Carolina at Charlotte, Charlotte, NC 28223, USA.
| | - Nikolay V Dokholyan
- Department of Pharmacology, Penn State College of Medicine, Hershey, PA 17033-0850, USA; Department of Biochemistry & Molecular Biology, Penn State College of Medicine, Hershey, PA 17033-0850, USA.
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15
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Danai L, Johnson MB, Afonin KA. Discriminating Immunorecognition Pathways Activated by RNA Nanostructures. Methods Mol Biol 2023; 2709:229-240. [PMID: 37572284 PMCID: PMC10482317 DOI: 10.1007/978-1-0716-3417-2_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/14/2023]
Abstract
Nucleic acid nanoparticles (NANPs) composed of therapeutic DNA, RNA, or a hybrid of both are increasingly investigated for their targeted and tunable immunomodulatory properties. By taking advantage of the NANPs' unique and relatively straightforward self-assembling behavior, nucleic acid sequences can be designed from the bottom-up and specifically tailored to induce certain immune responses in mammalian cells (Johnson et al., Nucleic Acids Res 48:11785-11798, 2020). Although not yet used in the clinic, functionalized NANPs display promising advantages to be included in therapeutic applications. By adjusting the chemical composition of a limited selection of NANPs all sharing the same physicochemical properties, it is demonstrated how substituting RNA strands for different chemical analogs can increase the thermodynamic and enzymatic stability of NANPs. Altering the composition of NANPs also determines the cellular mechanisms which initiate immune responses, therefore impacting the subcellular targeting and delivery efficiency.
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Affiliation(s)
- Leyla Danai
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, NC, USA
| | - M Brittany Johnson
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, NC, USA
| | - Kirill A Afonin
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, NC, USA.
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16
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Avila YI, Rebolledo L, Andrade-Muñoz M, Afonin KA. Characterization of PAMAM Dendrimers for the Delivery of Nucleic Acid Nanoparticles. Methods Mol Biol 2023; 2709:253-259. [PMID: 37572286 PMCID: PMC10482315 DOI: 10.1007/978-1-0716-3417-2_17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/14/2023]
Abstract
The protocols described in this book chapter are meant to be used as an outline and guideline to explore the use of a cationic, polymeric, and synthetic carrier-poly (amidoamine) (PAMAM) dendrimers. The amine-terminated, hyperbranched structures have been identified as a vehicle for the delivery of nucleic acids. As such, clear protocols for the optimization of dendrimer usage should be set in place. This chapter details the experiments used to determine the ratio that dendrimers and nucleic acids should be complexed at through the use of binding assays, nuclease protection assays, and competitive binding assays.
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Affiliation(s)
- Yelixza I Avila
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, NC, USA
| | - Laura Rebolledo
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, NC, USA
| | - Melanie Andrade-Muñoz
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, NC, USA
| | - Kirill A Afonin
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, NC, USA.
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17
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Radwan Y, Rebolledo LP, Panigaj M, Afonin KA. Dynamic Nanostructures for Conditional Activation and Deactivation of Biological Pathways. Methods Mol Biol 2023; 2709:309-318. [PMID: 37572291 PMCID: PMC10482318 DOI: 10.1007/978-1-0716-3417-2_22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/14/2023]
Abstract
Nucleic acid nanotechnology utilizes natural and synthetic structural motifs to build versatile nucleic acid nanoparticles (NANPs). These rationally designed assemblies can be further equipped with functional nucleic acids and other molecules such as peptides, fluorescent dyes, etc. In addition to nucleic acids that directly interact with the regulated target gene transcripts, NANPs can display decoys, wherein the oligonucleotide stretches with transcription factor binding sequences, preventing transcription initiation. The nuclear factor kappa-light-chain-enhancer of activated B cells (NF-κB) is a group of five crucial transcription factors regulating the pathogenesis of inflammatory diseases and cancer; as such, they are relevant targets for therapy. One therapeutic approach involves interdependent self-recognizing hybridized DNA/RNA fibers designed to bind NF-κB and prevent its interaction with the promotor region of NF-κB-dependent genes involved in inflammatory responses. Decoying NF-κB results in the inability to initiate transcription of regulated genes, showing a promising approach to gene regulation and gene therapy. The protocol described herein provides detailed steps for the synthesis of NF-κB decoy fibers, as well as their characterization using polyacrylamide gel electrophoresis (to confirm desired physicochemical properties and purity) and functional bioassays (to confirm desired biological activity).
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Affiliation(s)
- Yasmine Radwan
- Department of Chemistry, University of North Carolina, Charlotte, NC, USA
| | - Laura P Rebolledo
- Department of Chemistry, University of North Carolina, Charlotte, NC, USA
- Department of Biological Sciences, University of North Carolina, Charlotte, NC, USA
| | - Martin Panigaj
- Department of Chemistry, University of North Carolina, Charlotte, NC, USA
| | - Kirill A Afonin
- Department of Chemistry, University of North Carolina, Charlotte, NC, USA.
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18
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Beasock D, Afonin KA. Structural Characterization of DNA-Templated Silver Nanoclusters by Energy Dispersive Spectroscopy. Methods Mol Biol 2023; 2709:163-178. [PMID: 37572279 PMCID: PMC10482312 DOI: 10.1007/978-1-0716-3417-2_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/14/2023]
Abstract
Here, a novel method of structural determination for DNA-templated silver nanoclusters (DNA-AgNCs) is introduced. This technique uses energy dispersive spectroscopy (EDS) coupled with a scanning electron microscope (SEM) to analyze a monodisperse solution of nucleic acid-based structures. Exploiting the consistent number of phosphate atoms in each structure, we determine the average number of silver atoms that make up the DNA-AgNCs. Proper sample preparation and fine-tuning of the SEM/EDS system settings were combined to achieve highly repeatable data.
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Affiliation(s)
- Damian Beasock
- University of North Carolina at Charlotte, Charlotte, NC, USA
| | - Kirill A Afonin
- University of North Carolina at Charlotte, Charlotte, NC, USA.
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19
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Rolband LA, Ke W, Afonin KA. Aptamer Conjugated RNA/DNA Hybrid Nanostructures Designed for Efficient Regulation of Blood Coagulation. Methods Mol Biol 2023; 2709:277-286. [PMID: 37572288 PMCID: PMC10498824 DOI: 10.1007/978-1-0716-3417-2_19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/14/2023]
Abstract
Disruptions to the hemostatic pathway can cause a variety of serious or even life-threatening complications. Situations in which the coagulation of blood has become disturbed necessitate immediate care. Thrombin-binding aptamers are single-stranded nucleic acids that bind to thrombin with high specificity and affinity. While they can effectively inhibit thrombin, they suffer from rapid degradation and clearance in vivo. These issues are resolved, however, by attaching the therapeutic aptamer to a nucleic acid nanostructure. The increased size of the nanostructure-aptamer complex elongates the post-infusion half-life of the aptamer. These complexes are also immunoquiescent. A significant benefit of using nucleic acids as anticoagulants is their rapid deactivation by the introduction of a nanostructure made fully from the reverse complement of the therapeutically active nanostructure. These advantages make nanoparticle conjugated antithrombin aptamers a promising candidate for a rapidly reversible anticoagulant therapy.
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Affiliation(s)
- Lewis A Rolband
- University of North Carolina at Charlotte, Charlotte, NC, USA
| | - Weina Ke
- University of North Carolina at Charlotte, Charlotte, NC, USA
| | - Kirill A Afonin
- University of North Carolina at Charlotte, Charlotte, NC, USA.
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20
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Panigaj M, Skelly E, Beasock D, Marriott I, Johnson MB, Salotti J, Afonin KA. Therapeutic immunomodulation by rationally designed nucleic acids and nucleic acid nanoparticles. Front Immunol 2023; 14:1053550. [PMID: 36798121 PMCID: PMC9927404 DOI: 10.3389/fimmu.2023.1053550] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2022] [Accepted: 01/18/2023] [Indexed: 02/01/2023] Open
Abstract
The immune system has evolved to defend organisms against exogenous threats such as viruses, bacteria, fungi, and parasites by distinguishing between "self" and "non-self". In addition, it guards us against other diseases, such as cancer, by detecting and responding to transformed and senescent cells. However, for survival and propagation, the altered cells and invading pathogens often employ a wide range of mechanisms to avoid, inhibit, or manipulate the immunorecognition. As such, the development of new modes of therapeutic intervention to augment protective and prevent harmful immune responses is desirable. Nucleic acids are biopolymers essential for all forms of life and, therefore, delineating the complex defensive mechanisms developed against non-self nucleic acids can offer an exciting avenue for future biomedicine. Nucleic acid technologies have already established numerous approaches in therapy and biotechnology; recently, rationally designed nucleic acids nanoparticles (NANPs) with regulated physiochemical properties and biological activities has expanded our repertoire of therapeutic options. When compared to conventional therapeutic nucleic acids (TNAs), NANP technologies can be rendered more beneficial for synchronized delivery of multiple TNAs with defined stabilities, immunological profiles, and therapeutic functions. This review highlights several recent advances and possible future directions of TNA and NANP technologies that are under development for controlled immunomodulation.
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Affiliation(s)
- Martin Panigaj
- Nanoscale Science Program, Department of Chemistry, The University of North Carolina at Charlotte, Charlotte, NC, United States.,Institute of Biology & Ecology, Faculty of Science, Pavol Jozef Safarik University in Kosice, Kosice, Slovakia
| | - Elizabeth Skelly
- Nanoscale Science Program, Department of Chemistry, The University of North Carolina at Charlotte, Charlotte, NC, United States
| | - Damian Beasock
- Nanoscale Science Program, Department of Chemistry, The University of North Carolina at Charlotte, Charlotte, NC, United States
| | - Ian Marriott
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, NC, United States
| | - M Brittany Johnson
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, NC, United States
| | - Jacqueline Salotti
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, Frederick, MD, United States
| | - Kirill A Afonin
- Nanoscale Science Program, Department of Chemistry, The University of North Carolina at Charlotte, Charlotte, NC, United States
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21
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Byrnes J, Chopra K, Rolband LA, Danai L, Chodankar S, Yang L, Afonin KA. Structural Characterization of Nucleic Acid Nanoparticles Using SAXS and SAXS-Driven MD. Methods Mol Biol 2023; 2709:65-94. [PMID: 37572273 PMCID: PMC10484297 DOI: 10.1007/978-1-0716-3417-2_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/14/2023]
Abstract
Structural characterization of nucleic acid nanoparticles (NANPs) in solution is critical for validation of correct assembly and for quantifying the size, shape, and flexibility of the construct. Small-angle X-ray scattering (SAXS) is a well-established method to obtain structural information of particles in solution. Here, we present a procedure for the preparation of NANPs for SAXS. This procedure outlines the steps for a successful SAXS experiment and the use of SAXS-driven molecular dynamics to generate an ensemble of structures that best explain the data observed in solution. We use an RNA NANP as an example, so the reader can prepare the sample for data collection, analyze the results, and perform SAXS-driven MD on similar NANPs.
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Affiliation(s)
| | | | - Lewis A Rolband
- University of North Carolina at Charlotte, Charlotte, NC, USA
| | - Leyla Danai
- University of North Carolina at Charlotte, Charlotte, NC, USA
| | | | - Lin Yang
- Brookhaven National Laboratory, Upton, NY, USA
| | - Kirill A Afonin
- University of North Carolina at Charlotte, Charlotte, NC, USA
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22
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Skelly E, Rolband LA, Beasock D, Afonin KA. Synthesis of DNA-Templated Silver Nanoclusters and the Characterization of Their Optical Properties and Biological Activity. Methods Mol Biol 2023; 2709:299-307. [PMID: 37572290 PMCID: PMC10482316 DOI: 10.1007/978-1-0716-3417-2_21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/14/2023]
Abstract
DNA-templated silver nanoclusters (DNA-AgNCs) are a unique class of bioinorganic nanomaterials. The optical properties and biological activities of DNA-AgNCs are readily modulated by the minor adjustments in the sequence or structure of the templating oligonucleotide. Excitation-emission matrix spectroscopy (EEMS) enables the fluorescence of compounds to be measured in a way that examines the entirety of a material's fluorescent properties. The use of EEMS for the characterization of DNA-AgNCs allows for multiple fluorescence peaks to be readily identified while providing the excitation and emission wavelengths of each signal. To assess the antibacterial and cytotoxic activities of DNA-AgNCs, two separate experimental approaches are used. Assessing the growth of bacteria over time is accomplished by measuring the optical density of the bacterial suspension with 600 nm light, which is directly related to the number of bacteria in suspension. In order to evaluate the DNA-AgNCs for cytotoxic activity, cell viability assays which probe mitochondrial activity were used. Herein, we describe protocols for the characterization of the fluorescent, antibacterial, and cytotoxic activities of DNA-AgNCs using EEM, optical density measurements, and cell viability assays.
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23
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Gupta AK, Petersen J, Skelly E, Afonin KA, Krasnoslobodtsev AV. Small Volume Microrheology to Evaluate Viscoelastic Properties of Nucleic Acid-Based Supra-Assemblies. Methods Mol Biol 2023; 2709:179-189. [PMID: 37572280 PMCID: PMC10482311 DOI: 10.1007/978-1-0716-3417-2_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/14/2023]
Abstract
Particle tracking (PT) microrheology is a passive microrheological approach that characterizes material properties of soft matter. Multicomponent materials with the ability to create extensive crosslinking, such as supra-assemblies, may exhibit a complex interplay of viscous and elastic properties with a substantial contribution of liquid phase still diffusing through the system. Microrheology analyzes the motion of microscopic beads immersed in a sample, making it possible to evaluate the rheological properties of biological supra-assemblies. This method requires only a small volume of the sample and a relatively simple, inexpensive experimental setup. The objective of this chapter is to describe the experimental procedures for the observation of particle motion, calibration of an optical setup for particle tracking, preparation of imaging chambers, and the use of image analysis software for particle tracking in viscoelastic nucleic acid-based supra-assemblies.
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Affiliation(s)
| | - Joel Petersen
- Department of Physics, University of Nebraska Omaha, Omaha, NE, USA
| | - Elizabeth Skelly
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, NC, USA
| | - Kirill A Afonin
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, NC, USA
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24
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de Freitas Saito R, Barion BG, da Rocha TRF, Rolband A, Afonin KA, Chammas R. Anticoagulant Activity of Nucleic Acid Nanoparticles (NANPs) Assessed by Thrombin Generation Dynamics on a Fully Automated System. Methods Mol Biol 2023; 2709:319-332. [PMID: 37572292 PMCID: PMC10482313 DOI: 10.1007/978-1-0716-3417-2_23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/14/2023]
Abstract
Rapidly reversible anticoagulant agents have great clinical potential. Oligonucleotide-based anticoagulant agents are uniquely positioned to fill this clinical niche, as they are able to be deactivated through the introduction of the reverse complement oligo. Once the therapeutic and the antidote oligos meet in solution, they are able to undergo isothermal reassociation to form short, inactive, duplexes that are rapidly secreted via filtration by the kidneys. The formation of the duplexes interrupts the structure of the anticoagulant oligo, allowing normal coagulation to be restored. To effectively assess these new anticoagulants, a variety of methods may be employed. The measurement of thrombin generation (TG) reflects the overall capacity of plasma to produce active thrombin and provides a strong contribution to identifying new anticoagulant drugs, including DNA/RNA thrombin binding aptamer carrying fibers which are used through this chapter as an example. Here we describe the TG assessed by Calibrated Automated Thrombogram (CAT) assay in a fully automated system. This method is based on the detection of TG in plasma samples by measuring fluorescent signals released from a quenched fluorogenic thrombin substrate and the subsequent conversion of these signals in TG curves.
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Affiliation(s)
- Renata de Freitas Saito
- Comprehensive Center for Precision Oncology, Centro de Investigação Translacional em Oncologia (LIM24), Departamento de Radiologia e Oncologia, Faculdade de Medicina da Universidade de São Paulo and Instituto do Câncer do Estado de São Paulo, São Paulo, SP, Brazil.
| | - Bárbara Gomes Barion
- Laboratório de Hemostasia do Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, São Paulo, SP, Brazil
| | - Tania Rubia Flores da Rocha
- Laboratório de Hemostasia do Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, São Paulo, SP, Brazil
| | - Alex Rolband
- University of North Carolina, Charlotte, NC, USA
| | | | - Roger Chammas
- Comprehensive Center for Precision Oncology, Centro de Investigação Translacional em Oncologia (LIM24), Departamento de Radiologia e Oncologia, Faculdade de Medicina da Universidade de São Paulo and Instituto do Câncer do Estado de São Paulo, São Paulo, SP, Brazil.
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Radwan Y, Afonin KA, Johnson MB. Assessment of Intracellular Compartmentalization of RNA Nanostructures. Methods Mol Biol 2023; 2709:211-228. [PMID: 37572283 PMCID: PMC10482314 DOI: 10.1007/978-1-0716-3417-2_14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/14/2023]
Abstract
Nucleic acid nanoparticles (NANPs) are extensively investigated as diagnostic and therapeutic tools. These innovative particles can be composed of RNA, DNA, and/or modified nucleic acids. Due to the regulatory role of nucleic acids in the cellular system, NANPs have the ability to identify target molecules and regulate expression of genes in disease pathways. However, translation of NANPs in clinical settings is hindered due to inefficient intracellular delivery, chemical instability, and off-target immunostimulatory effects following immune recognition. The composition of nucleic acids forming NANPs has been demonstrated to influence immunorecognition, subcellular compartmentalization, and physicochemical properties of NANPs. This chapter first outlines the methods used to generate a panel of NANPs with a uniform shape, size, charge, sequence, and connectivity. This includes the procedures for replacing the RNA strands with DNA or chemical analogs in the designated NANPs. Second, this chapter will also describe experiments to assess the effect of the chemical modification on enzymatic and thermodynamic stability, delivery efficiency, and subcellular compartmentalization of NANPs.
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Affiliation(s)
- Yasmine Radwan
- Department of Chemistry, University of North Carolina at Charlotte, Charlotte, NC, USA
| | - Kirill A Afonin
- Department of Chemistry, University of North Carolina at Charlotte, Charlotte, NC, USA
| | - M Brittany Johnson
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, NC, USA.
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26
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Lushnikov AJ, Avila YI, Afonin KA, Krasnoslobodtsev AV. Characterization of RNA Nanoparticles and Their Dynamic Properties Using Atomic Force Microscopy. Methods Mol Biol 2023; 2709:191-202. [PMID: 37572281 PMCID: PMC10483931 DOI: 10.1007/978-1-0716-3417-2_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/14/2023]
Abstract
The protocol described in this chapter allows for acquiring topography images of RNA-based nanoring structures and assessing their dynamic properties using atomic force microscopy (AFM) imaging. AFM is an indispensable tool for characterization of nucleic acid-based nanostructures with the exceptional capability of observing complexes in the range of a few nanometers. This method can visualize structural characteristics and evaluate differences between individual structurally different RNA nanorings. Due to the highly resolved AFM topography images, we introduce an approach that allows to distinguish the differences in the dynamic behavior of RNA nanoparticles not amenable to other experimental techniques. This protocol describes in detail the preparation procedures of RNA nanostructures, AFM imaging, and data analysis.
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Affiliation(s)
- Alexander J Lushnikov
- Nanoimaging Core Facility at the University of Nebraska Medical Center, Omaha, NE, USA
| | - Yelixza I Avila
- Department of Chemistry, Nanoscale Science Program, University of North Carolina, Charlotte, NC, USA
| | - Kirill A Afonin
- Department of Chemistry, Nanoscale Science Program, University of North Carolina, Charlotte, NC, USA
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27
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Vishweshwaraiah YL, Hnath B, Rackley B, Wang J, Gontu A, Chandler M, Afonin KA, Kuchipudi SV, Christensen N, Yennawar NH, Dokholyan NV. Adaptation-proof SARS-CoV-2 vaccine design. Adv Funct Mater 2022; 32:2206055. [PMID: 36590650 PMCID: PMC9799234 DOI: 10.1002/adfm.202206055] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) surface spike glycoprotein - a major antibody target - is critical for virus entry via engagement of human angiotensin-converting enzyme 2 (ACE2) receptor. Despite successes with existing vaccines and therapies that primarily target the receptor binding domain (RBD) of the spike protein, the susceptibility of RBD to mutations provides escape routes for the SARS-CoV-2 from neutralizing antibodies. On the other hand, structural conservation in the spike protein can be targeted to reduce escape mutations and achieve broad protection. Here, we designed candidate stable immunogens that mimic surface features of selected conserved regions of spike protein through 'epitope grafting,' in which we present the target epitope topology on diverse heterologous scaffolds that can structurally accommodate the spike epitopes. Structural characterization of the epitope-scaffolds showed stark agreement with our computational models and target epitopes. The sera from mice immunized with engineered designs display epitope-scaffolds and spike binding activity. We also demonstrated the utility of the designed epitope-scaffolds in diagnostic applications. Taken all together, our study provides important methodology for targeting the conserved, non-RBD structural motifs of spike protein for SARS-CoV-2 epitope vaccine design and demonstrates the potential utility of 'epitope grafting' in rational vaccine design.
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Affiliation(s)
| | - Brianna Hnath
- Department of PharmacologyPenn State College of MedicineHersheyPA17033‐0850USA
| | - Brendan Rackley
- Department of PharmacologyPenn State College of MedicineHersheyPA17033‐0850USA
| | - Jian Wang
- Department of PharmacologyPenn State College of MedicineHersheyPA17033‐0850USA
| | - Abhinay Gontu
- Department of Veterinary and Biomedical Sciences and The Huck Institutes of the Life SciencesThe Pennsylvania State UniversityUniversity ParkPA16802USA
| | - Morgan Chandler
- Department of ChemistryUniversity of North Carolina at CharlotteCharlotteNC28223USA
| | - Kirill A. Afonin
- Department of ChemistryUniversity of North Carolina at CharlotteCharlotteNC28223USA
| | - Suresh V. Kuchipudi
- Department of Veterinary and Biomedical Sciences and The Huck Institutes of the Life SciencesThe Pennsylvania State UniversityUniversity ParkPA16802USA
| | - Neil Christensen
- Department of Microbiology and ImmunologyPenn State College of MedicineHersheyPA17033‐0850USA
| | - Neela H. Yennawar
- The Huck Institutes of the Life SciencesThe Pennsylvania State UniversityUniversity ParkPA16802USA
| | - Nikolay V. Dokholyan
- Department of PharmacologyPenn State College of MedicineHersheyPA17033‐0850USA
- Department of Biochemistry & Molecular BiologyPenn State College of MedicineHersheyPA17033‐0850USA
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Chandler M, Jain S, Halman J, Hong E, Dobrovolskaia MA, Zakharov AV, Afonin KA. Artificial Immune Cell, AI-cell, a New Tool to Predict Interferon Production by Peripheral Blood Monocytes in Response to Nucleic Acid Nanoparticles. Small 2022; 18:e2204941. [PMID: 36216772 PMCID: PMC9671856 DOI: 10.1002/smll.202204941] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 09/15/2022] [Indexed: 06/16/2023]
Abstract
Nucleic acid nanoparticles, or NANPs, rationally designed to communicate with the human immune system, can offer innovative therapeutic strategies to overcome the limitations of traditional nucleic acid therapies. Each set of NANPs is unique in their architectural parameters and physicochemical properties, which together with the type of delivery vehicles determine the kind and the magnitude of their immune response. Currently, there are no predictive tools that would reliably guide the design of NANPs to the desired immunological outcome, a step crucial for the success of personalized therapies. Through a systematic approach investigating physicochemical and immunological profiles of a comprehensive panel of various NANPs, the research team developes and experimentally validates a computational model based on the transformer architecture able to predict the immune activities of NANPs. It is anticipated that the freely accessible computational tool that is called an "artificial immune cell," or AI-cell, will aid in addressing the current critical public health challenges related to safety criteria of nucleic acid therapies in a timely manner and promote the development of novel biomedical tools.
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Affiliation(s)
- Morgan Chandler
- Department of Chemistry, University of North Carolina at Charlotte, Charlotte, NC 28223, USA
| | - Sankalp Jain
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD 20850, USA
| | - Justin Halman
- Department of Chemistry, University of North Carolina at Charlotte, Charlotte, NC 28223, USA
| | - Enping Hong
- Nanotechnology Characterization Lab, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Marina A. Dobrovolskaia
- Nanotechnology Characterization Lab, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Alexey V. Zakharov
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD 20850, USA
| | - Kirill A. Afonin
- Department of Chemistry, University of North Carolina at Charlotte, Charlotte, NC 28223, USA
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Chandler M, Rolband L, Johnson MB, Shi D, Avila YI, Cedrone E, Beasock D, Danai L, Stassenko E, Krueger JK, Jiang J, Lee JS, Dobrovolskaia MA, Afonin KA. Expanding Structural Space for Immunomodulatory Nucleic Acid Nanoparticles (Nanps) via Spatial Arrangement of Their Therapeutic Moieties. Adv Funct Mater 2022; 32:2205581. [PMID: 37008199 PMCID: PMC10065476 DOI: 10.1002/adfm.202205581] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Indexed: 05/16/2023]
Abstract
Different therapeutic nucleic acids (TNAs) can be unified in a single structure by their elongation with short oligonucleotides designed to self-assemble into nucleic acid nanoparticles (NANPs). With this approach, therapeutic cocktails with precisely controlled composition and stoichiometry of active ingredients can be delivered to the same diseased cells for enhancing pharmaceutical action. In this work, an additional nanotechnology-based therapeutic option that enlists a biocompatible NANP-encoded platform for their controlled patient-specific immunorecognition is explored. For this, a set of representative functional NANPs is extensively characterized in vitro, ex vivo, and in vivo and then further analyzed for immunostimulation of human peripheral blood mononuclear cells freshly collected from healthy donor volunteers. The results of the study present the advancement of the current TNA approach toward personalized medicine and offer a new strategy to potentially address top public health challenges related to drug overdose and safety through the biodegradable nature of the functional platform with immunostimulatory regulation.
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Affiliation(s)
- Morgan Chandler
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, NC 28223, USA
| | - Lewis Rolband
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, NC 28223, USA
| | - M Brittany Johnson
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, NC 28223, USA
| | - Da Shi
- Nanotechnology Characterization Laboratory, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Yelixza I Avila
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, NC 28223, USA
| | - Edward Cedrone
- Nanotechnology Characterization Laboratory, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Damian Beasock
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, NC 28223, USA
| | - Leyla Danai
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, NC 28223, USA
| | - Elizabeth Stassenko
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, NC 28223, USA
| | - Joanna K Krueger
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, NC 28223, USA
| | - Jiancheng Jiang
- Department of Mathematics, University of North Carolina at Charlotte, Charlotte, NC 28223, USA
| | - Jeoung Soo Lee
- Drug Design, Development, and Delivery (4D) Laboratory, Department of Bioengineering, Clemson University, Clemson, SC 29634, USA
| | - Marina A Dobrovolskaia
- Nanotechnology Characterization Laboratory, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Kirill A Afonin
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, NC 28223, USA
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Anh Lam P, Furr DP, Tran A, McKeough RQ, Beasock D, Chandler M, Afonin KA, Trammell SR. The Application of Light-Assisted Drying to the Thermal Stabilization of Nucleic Acid Nanoparticles. Biopreserv Biobank 2022; 20:451-460. [PMID: 36067075 PMCID: PMC9603253 DOI: 10.1089/bio.2022.0035] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Background: Cold-chain storage can be challenging and expensive for the transportation and storage of biologics, especially in low-resource settings. Nucleic acid nanoparticles (NANPs) are an example of new biological products that require refrigerated storage. Light-assisted drying (LAD) is a new processing technique to prepare biologics for anhydrous storage in a trehalose amorphous solid matrix at ambient temperatures. In this study, LAD was used to thermally stabilize four types of NANPs with differing structures and melting temperatures. Methods: Small volume samples (10 μL) containing NANPs were irradiated with a 1064 nm laser to speed the evaporation of water and create an amorphous trehalose preservation matrix. Samples were then stored for 1 month at 4°C or 20°C. A FLIR C655 mid-IR camera was used to record the temperature of samples during processing. The trehalose matrix was characterized using polarized light imaging (PLI) to determine if crystallization occurred during processing or storage. Damage to LAD-processed NANPs was assessed after processing and storage using gel electrophoresis. Results: Based on the end moisture content (EMC) as a function time and the thermal histories of samples, a LAD processing time of 30 min is sufficient to achieve low EMCs for the 10 μL samples used in this study. PLI demonstrates that the trehalose matrix was resistant to crystallization during processing and after storage at 4°C and at room temperature. The native-polyacrylamide gel electrophoresis results for DNA cubes, RNA cubes, and RNA rings indicate that the main structures of these NANPs were not damaged significantly after LAD processing and being stored at 4°C or at room temperature for 1 month. Conclusions: These preliminary studies indicate that LAD processing can stabilize NANPs for dry-state storage at room temperature, providing an alternative to refrigerated storage for these nanomedicine products.
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Affiliation(s)
- Phuong Anh Lam
- Department of Physics and Optical Science and University of North Carolina at Charlotte, Charlotte, North Carolina, USA
| | - Daniel P. Furr
- Department of Physics and Optical Science and University of North Carolina at Charlotte, Charlotte, North Carolina, USA
| | - Allison Tran
- Department of Chemistry, University of North Carolina at Charlotte, Charlotte, North Carolina, USA
| | - Riley Q. McKeough
- Department of Physics and Optical Science and University of North Carolina at Charlotte, Charlotte, North Carolina, USA
| | - Damian Beasock
- Department of Chemistry, University of North Carolina at Charlotte, Charlotte, North Carolina, USA
| | - Morgan Chandler
- Department of Chemistry, University of North Carolina at Charlotte, Charlotte, North Carolina, USA
| | - Kirill A. Afonin
- Department of Chemistry, University of North Carolina at Charlotte, Charlotte, North Carolina, USA
| | - Susan R. Trammell
- Department of Physics and Optical Science and University of North Carolina at Charlotte, Charlotte, North Carolina, USA
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Ke W, Chandler M, Cedrone E, Saito RF, Rangel MC, de Souza Junqueira M, Wang J, Shi D, Truong N, Richardson M, Rolband LA, Dréau D, Bedocs P, Chammas R, Dokholyan NV, Dobrovolskaia MA, Afonin KA. Locking and Unlocking Thrombin Function Using Immunoquiescent Nucleic Acid Nanoparticles with Regulated Retention In Vivo. Nano Lett 2022; 22:5961-5972. [PMID: 35786891 PMCID: PMC9511123 DOI: 10.1021/acs.nanolett.2c02019] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The unbalanced coagulation of blood is a life-threatening event that requires accurate and timely treatment. We introduce a user-friendly biomolecular platform based on modular RNA-DNA anticoagulant fibers programmed for reversible extracellular communication with thrombin and subsequent control of anticoagulation via a "kill-switch" mechanism that restores hemostasis. To demonstrate the potential of this reconfigurable technology, we designed and tested a set of anticoagulant fibers that carry different thrombin-binding aptamers. All fibers are immunoquiescent, as confirmed in freshly collected human peripheral blood mononuclear cells. To assess interindividual variability, the anticoagulation is confirmed in the blood of human donors from the U.S. and Brazil. The anticoagulant fibers reveal superior anticoagulant activity and prolonged renal clearance in vivo in comparison to free aptamers. Finally, we confirm the efficacy of the "kill-switch" mechanism in vivo in murine and porcine models.
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Affiliation(s)
- Weina Ke
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, North Carolina 28223, United States
| | - Morgan Chandler
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, North Carolina 28223, United States
| | - Edward Cedrone
- Nanotechnology Characterization Lab., Cancer Research Technology Program, Frederick National Laboratory for Cancer Research sponsored by the National Cancer Institute, Frederick, Maryland 21702, United States
| | - Renata F Saito
- Centro de Investigação Translacional em Oncologia (LIM24), Departamento de Radiologia e Oncologia, Faculdade de Medicina da Universidade de São Paulo and Instituto do Câncer do Estado de São Paulo, São Paulo, SP 01246-903, Brazil
| | - Maria Cristina Rangel
- Centro de Investigação Translacional em Oncologia (LIM24), Departamento de Radiologia e Oncologia, Faculdade de Medicina da Universidade de São Paulo and Instituto do Câncer do Estado de São Paulo, São Paulo, SP 01246-903, Brazil
| | - Mara de Souza Junqueira
- Centro de Investigação Translacional em Oncologia (LIM24), Departamento de Radiologia e Oncologia, Faculdade de Medicina da Universidade de São Paulo and Instituto do Câncer do Estado de São Paulo, São Paulo, SP 01246-903, Brazil
| | - Jian Wang
- Department of Pharmacology, Department of Biochemistry & Molecular Biology, Penn State College of Medicine, Hershey, Pennsylvania 17033, United States
| | - Da Shi
- Nanotechnology Characterization Lab., Cancer Research Technology Program, Frederick National Laboratory for Cancer Research sponsored by the National Cancer Institute, Frederick, Maryland 21702, United States
| | - Nguyen Truong
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, North Carolina 28223, United States
| | - Melina Richardson
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, North Carolina 28223, United States
| | - Lewis A Rolband
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, North Carolina 28223, United States
| | - Didier Dréau
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, North Carolina 28223, United States
| | - Peter Bedocs
- Department of Anesthesiology, School of Medicine, Uniformed Services University of the Health Sciences, Bethesda, Maryland 20814, United States
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, Maryland 20817, United States
| | - Roger Chammas
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, North Carolina 28223, United States
- Centro de Investigação Translacional em Oncologia (LIM24), Departamento de Radiologia e Oncologia, Faculdade de Medicina da Universidade de São Paulo and Instituto do Câncer do Estado de São Paulo, São Paulo, SP 01246-903, Brazil
| | - Nikolay V Dokholyan
- Department of Pharmacology, Department of Biochemistry & Molecular Biology, Penn State College of Medicine, Hershey, Pennsylvania 17033, United States
- Department of Chemistry, Department of Biomedical Engineering, Penn State University, University Park, Pennsylvania 16802, United States
| | - Marina A Dobrovolskaia
- Nanotechnology Characterization Lab., Cancer Research Technology Program, Frederick National Laboratory for Cancer Research sponsored by the National Cancer Institute, Frederick, Maryland 21702, United States
| | - Kirill A Afonin
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, North Carolina 28223, United States
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Vishweshwaraiah YL, Hnath B, Rackley B, Wang J, Gontu A, Chandler M, Afonin KA, Kuchipudi SV, Christensen N, Yennawar NH, Dokholyan NV. Adaptation-proof SARS-CoV-2 vaccine design. bioRxiv 2022:2022.05.17.492310. [PMID: 35611332 PMCID: PMC9128779 DOI: 10.1101/2022.05.17.492310] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) surface spike glycoprotein - a major antibody target - is critical for virus entry via engagement of human angiotensin-converting enzyme 2 (ACE2) receptor. Despite successes with existing vaccines and therapies that primarily target the receptor binding domain (RBD) of the spike protein, the susceptibility of RBD to mutations provides escape routes for the SARS-CoV-2 from neutralizing antibodies. On the other hand, structural conservation in the spike protein can be targeted to reduce escape mutations and achieve broad protection. Here, we designed candidate stable immunogens that mimic surface features of selected conserved regions of spike protein through 'epitope grafting,' in which we present the target epitope topology on diverse heterologous scaffolds that can structurally accommodate the spike epitopes. Structural characterization of the epitope-scaffolds showed stark agreement with our computational models and target epitopes. The sera from mice immunized with engineered designs display epitope-scaffolds and spike binding activity. We also demonstrated the utility of the designed epitope-scaffolds in diagnostic applications. Taken all together, our study provides important methodology for targeting the conserved, non-RBD structural motifs of spike protein for SARS-CoV-2 epitope vaccine design and demonstrates the potential utility of 'epitope grafting' in rational vaccine design.
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Tripathi P, Chandler M, Maffeo CM, Fallahi A, Makhamreh A, Halman J, Aksimentiev A, Afonin KA, Wanunu M. Discrimination of RNA fiber structures using solid-state nanopores. Nanoscale 2022; 14:6866-6875. [PMID: 35441627 PMCID: PMC9520586 DOI: 10.1039/d1nr08002d] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
RNA fibers are a class of biomaterials that can be assembled using HIV-like kissing loop interactions. Because of the programmability of molecular design and low immunorecognition, these structures present an interesting opportunity to solve problems in nanobiotechnology and synthetic biology. However, the experimental tools to fully characterize and discriminate among different fiber structures in solution are limited. Herein, we utilize solid-state nanopore experiments and Brownian dynamics simulations to characterize and distinguish several RNA fiber structures that differ in their degrees of branching. We found that, regardless of the electrolyte type and concentration, fiber structures that have more branches produce longer and deeper ionic current blockades in comparison to the unbranched fibers. Experiments carried out at temperatures ranging from 20-60 °C revealed almost identical distributions of current blockade amplitudes, suggesting that the kissing loop interactions in fibers are resistant to heating within this range.
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Affiliation(s)
- Prabhat Tripathi
- Department of Physics, Northeastern University, Boston, MA, 02115, USA.
| | - Morgan Chandler
- Department of Chemistry, University of North Carolina at Charlotte, Charlotte, NC 28223, USA.
| | | | - Ali Fallahi
- Department of Bioengineering, Northeastern University, Boston, MA, 02115, USA
| | - Amr Makhamreh
- Department of Bioengineering, Northeastern University, Boston, MA, 02115, USA
| | - Justin Halman
- Department of Chemistry, University of North Carolina at Charlotte, Charlotte, NC 28223, USA.
| | - Aleksei Aksimentiev
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois, 61801, USA
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, Illinois, 61801, USA.
| | - Kirill A Afonin
- Department of Chemistry, University of North Carolina at Charlotte, Charlotte, NC 28223, USA.
| | - Meni Wanunu
- Department of Physics, Northeastern University, Boston, MA, 02115, USA.
- Department of Bioengineering, Northeastern University, Boston, MA, 02115, USA
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Tran AN, Chandler M, Halman J, Beasock D, Fessler A, McKeough RQ, Lam PA, Furr DP, Wang J, Cedrone E, Dobrovolskaia MA, Dokholyan NV, Trammell SR, Afonin KA. Anhydrous Nucleic Acid Nanoparticles for Storage and Handling at Broad Range of Temperatures. Small 2022; 18:e2104814. [PMID: 35128787 PMCID: PMC8976831 DOI: 10.1002/smll.202104814] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 12/17/2021] [Indexed: 05/13/2023]
Abstract
Recent advances in nanotechnology now allow for the methodical implementation of therapeutic nucleic acids (TNAs) into modular nucleic acid nanoparticles (NANPs) with tunable physicochemical properties which can match the desired biological effects, provide uniformity, and regulate the delivery of multiple TNAs for combinatorial therapy. Despite the potential of novel NANPs, the maintenance of their structural integrity during storage and shipping remains a vital issue that impedes their broader applications. Cold chain storage is required to maintain the potency of NANPs in the liquid phase, which greatly increases transportation costs. To promote long-term storage and retention of biological activities at higher temperatures (e.g., +50 °C), a panel of representative NANPs is first exposed to three different drying mechanisms-vacuum concentration (SpeedVac), lyophilization (Lyo), and light-assisted drying (LAD)-and then rehydrated and analyzed. While SpeedVac primarily operates using heat, Lyo avoids temperature increases by taking advantage of pressure reduction and LAD involves a near-infrared laser for uniform drying in the presence of trehalose. This work compares and defines refinements crucial in formulating an optimal strategy for producing stable, fully functional NANPs and presents a forward advancement in their development for clinical applications.
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Affiliation(s)
- Allison N Tran
- Nanoscale Science Program, Department of Chemistry, The University of North Carolina at Charlotte, Charlotte, NC, 28223, USA
| | - Morgan Chandler
- Nanoscale Science Program, Department of Chemistry, The University of North Carolina at Charlotte, Charlotte, NC, 28223, USA
| | - Justin Halman
- Nanoscale Science Program, Department of Chemistry, The University of North Carolina at Charlotte, Charlotte, NC, 28223, USA
| | - Damian Beasock
- Nanoscale Science Program, Department of Chemistry, The University of North Carolina at Charlotte, Charlotte, NC, 28223, USA
| | - Adam Fessler
- Nanoscale Science Program, Department of Chemistry, The University of North Carolina at Charlotte, Charlotte, NC, 28223, USA
| | - Riley Q McKeough
- Department of Physics and Optical Science, The University of North Carolina at Charlotte, Charlotte, NC, 28223, USA
| | - Phuong Anh Lam
- Department of Physics and Optical Science, The University of North Carolina at Charlotte, Charlotte, NC, 28223, USA
| | - Daniel P Furr
- Department of Physics and Optical Science, The University of North Carolina at Charlotte, Charlotte, NC, 28223, USA
| | - Jian Wang
- Department of Pharmacology, Department of Biochemistry & Molecular Biology, Penn State College of Medicine, Hershey, PA, 17033, USA
| | - Edward Cedrone
- Nanotechnology Characterization Lab, Frederick National Laboratory for Cancer Research sponsored by the National Cancer Institute, Frederick, MD, 21702, USA
| | - Marina A Dobrovolskaia
- Nanotechnology Characterization Lab, Frederick National Laboratory for Cancer Research sponsored by the National Cancer Institute, Frederick, MD, 21702, USA
| | - Nikolay V Dokholyan
- Department of Pharmacology, Department of Biochemistry & Molecular Biology, Penn State College of Medicine, Hershey, PA, 17033, USA
| | - Susan R Trammell
- Department of Physics and Optical Science, The University of North Carolina at Charlotte, Charlotte, NC, 28223, USA
| | - Kirill A Afonin
- Nanoscale Science Program, Department of Chemistry, The University of North Carolina at Charlotte, Charlotte, NC, 28223, USA
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Afonin KA, Dobrovolskaia MA, Ke W, Grodzinski P, Bathe M. Critical review of nucleic acid nanotechnology to identify gaps and inform a strategy for accelerated clinical translation. Adv Drug Deliv Rev 2022; 181:114081. [PMID: 34915069 PMCID: PMC8886801 DOI: 10.1016/j.addr.2021.114081] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 12/06/2021] [Accepted: 12/08/2021] [Indexed: 01/01/2023]
Abstract
With numerous recent advances, the field of therapeutic nucleic acid nanotechnology is now poised for clinical translation supported by several examples of FDA-approved nucleic acid nanoformulations including two recent mRNA-based COVID-19 vaccines. Within this rapidly growing field, a new subclass of nucleic acid therapeutics called nucleic acid nanoparticles (NANPs) has emerged in recent years, which offers several unique properties distinguishing it from traditional therapeutic nucleic acids. Key unique aspects of NANPs include their well-defined 3D structure, their tunable multivalent architectures, and their ability to incorporate conditional activations of therapeutic targeting and release functions that enable diagnosis and therapy of cancer, regulation of blood coagulation disorders, as well as the development of novel vaccines, immunotherapies, and gene therapies. However, non-consolidated research developments of this highly interdisciplinary field create crucial barriers that must be overcome in order to impact a broader range of clinical indications. Forming a consortium framework for nucleic acid nanotechnology would prioritize and consolidate translational efforts, offer several unifying solutions to expedite their transition from bench-to-bedside, and potentially decrease the socio-economic burden on patients for a range of conditions. Herein, we review the unique properties of NANPs in the context of therapeutic applications and discuss their associated translational challenges.
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Affiliation(s)
- Kirill A Afonin
- Nanoscale Science Program, Department of Chemistry, The University of North Carolina at Charlotte, Charlotte, NC 28223, USA.
| | - Marina A Dobrovolskaia
- Nanotechnology Characterization Lab, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research sponsored by the National Cancer Institute, Frederick, MD 21702, USA
| | - Weina Ke
- Biomedical Informatics and Data Science Program, Frederick National Laboratory for Cancer Research sponsored by the National Cancer Institute, Frederick, MD 21702, USA
| | - Piotr Grodzinski
- Nanodelivery Systems and Devices Branch, Cancer Imaging Program, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Mark Bathe
- Department of Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA.
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Shi D, Beasock D, Fessler A, Szebeni J, Ljubimova JY, Afonin KA, Dobrovolskaia MA. To PEGylate or not to PEGylate: Immunological properties of nanomedicine's most popular component, polyethylene glycol and its alternatives. Adv Drug Deliv Rev 2022; 180:114079. [PMID: 34902516 PMCID: PMC8899923 DOI: 10.1016/j.addr.2021.114079] [Citation(s) in RCA: 133] [Impact Index Per Article: 66.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 12/01/2021] [Accepted: 12/03/2021] [Indexed: 01/03/2023]
Abstract
Polyethylene glycol or PEG has a long history of use in medicine. Many conventional formulations utilize PEG as either an active ingredient or an excipient. PEG found its use in biotechnology therapeutics as a tool to slow down drug clearance and shield protein therapeutics from undesirable immunogenicity. Nanotechnology field applies PEG to create stealth drug carriers with prolonged circulation time and decreased recognition and clearance by the mononuclear phagocyte system (MPS). Most nanomedicines approved for clinical use and experimental nanotherapeutics contain PEG. Among the most recent successful examples are two mRNA-based COVID-19 vaccines that are delivered by PEGylated lipid nanoparticles. The breadth of PEG use in a wide variety of over the counter (OTC) medications as well as in drug products and vaccines stimulated research which uncovered that PEG is not as immunologically inert as it was initially expected. Herein, we review the current understanding of PEG's immunological properties and discuss them in the context of synthesis, biodistribution, safety, efficacy, and characterization of PEGylated nanomedicines. We also review the current knowledge about immunological compatibility of other polymers that are being actively investigated as PEG alternatives.
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Key Words
- Poly(ethylene)glycol, PEG, immunogenicity, immunology, nanomedicine, toxicity, anti-PEG antibodies, hypersensitivity, synthesis, drug delivery, biotherapeutics
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Affiliation(s)
- Da Shi
- Nanotechnology Characterization Lab, Frederick National Laboratory for Cancer Research sponsored by the National Cancer Institute, Frederick MD, USA
| | - Damian Beasock
- University of North Carolina Charlotte; Charlotte, NC, USA
| | - Adam Fessler
- University of North Carolina Charlotte; Charlotte, NC, USA
| | | | | | | | - Marina A. Dobrovolskaia
- Nanotechnology Characterization Lab, Frederick National Laboratory for Cancer Research sponsored by the National Cancer Institute, Frederick MD, USA;,Corresponding author:
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Chandler M, Johnson B, Khisamutdinov E, Dobrovolskaia MA, Sztuba-Solinska J, Salem AK, Breyne K, Chammas R, Walter NG, Contreras LM, Guo P, Afonin KA. The International Society of RNA Nanotechnology and Nanomedicine (ISRNN): The Present and Future of the Burgeoning Field. ACS Nano 2021; 15:16957-16973. [PMID: 34677049 PMCID: PMC9023608 DOI: 10.1021/acsnano.0c10240] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
The International Society of RNA Nanotechnology and Nanomedicine (ISRNN) hosts an annual meeting series focused on presenting the latest research achievements involving RNA-based therapeutics and strategies, aiming to expand their current biomedical applications while overcoming the remaining challenges of the burgeoning field of RNA nanotechnology. The most recent online meeting hosted a series of engaging talks and discussions from an international cohort of leading nanotechnologists that focused on RNA modifications and modulation, dynamic RNA structures, overcoming delivery limitations using a variety of innovative platforms and approaches, and addressing the newly explored potential for immunomodulation with programmable nucleic acid nanoparticles. In this Nano Focus, we summarize the main discussion points, conclusions, and future directions identified during this two-day webinar as well as more recent advances to highlight and to accelerate this exciting field.
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Affiliation(s)
- Morgan Chandler
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, North Carolina 28223, United States
| | - Brittany Johnson
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, North Carolina 28223, United States
| | - Emil Khisamutdinov
- Department of Chemistry, Ball State University, Muncie, Indiana 47304, United States
| | - Marina A Dobrovolskaia
- Nanotechnology Characterization Lab, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research sponsored by the National Cancer Institute, Frederick, Maryland 21702, United States
| | - Joanna Sztuba-Solinska
- Department of Biological Sciences, Auburn University, 120 W. Samford Avenue, Rouse Life Sciences Building, Auburn, Alabama 36849, United States
| | - Aliasger K Salem
- Department of Pharmaceutical Sciences and Experimental Therapeutics, College of Pharmacy, University of Iowa, Iowa City, Iowa 52242, United States
| | - Koen Breyne
- Molecular Neurogenetics Unit, Department of Neurology and Center for Molecular Imaging Research, Department of Radiology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachussets 02114, United States
| | - Roger Chammas
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, North Carolina 28223, United States
- Centro de Investigação Translacional em Oncologia, Departamento de Radiologia e Oncologia, Instituto do Cancer do Estado de São Paulo - ICESP, Faculdade de Medicina da Universidade de São Paulo - FMUSP, Avenida Dr. Arnaldo 251, Cerqueira César, São Paulo 01246-000, São Paulo, Brazil
| | - Nils G Walter
- Single Molecule Analysis Group, Department of Chemistry and Center for RNA Biomedicine, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Lydia M Contreras
- McKetta Department of Chemical Engineering and Department of Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas 78714, United States
| | - Peixuan Guo
- Center for RNA Nanobiotechnology and Nanomedicine, College of Pharmacy, Division of Pharmaceutics and Pharmaceutical Chemistry, College of Medicine, Dorothy M. Davis Heart and Lung Research Institute, James Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio 43210, United States
| | - Kirill A Afonin
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, North Carolina 28223, United States
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38
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Ke W, Afonin KA. Exosomes as natural delivery carriers for programmable therapeutic nucleic acid nanoparticles (NANPs). Adv Drug Deliv Rev 2021; 176:113835. [PMID: 34144087 PMCID: PMC8440450 DOI: 10.1016/j.addr.2021.113835] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 06/10/2021] [Accepted: 06/12/2021] [Indexed: 02/06/2023]
Abstract
With recent advances in nanotechnology and therapeutic nucleic acids (TNAs), various nucleic acid nanoparticles (NANPs) have demonstrated great promise in diagnostics and therapeutics. However, the full realization of NANPs' potential necessitates the development of a safe, efficient, biocompatible, stable, tissue-specific, and non-immunogenic delivery system. Exosomes, the smallest extracellular vesicles and an endogenous source of nanocarriers, offer these advantages while avoiding complications associated with manufactured agents. The lipid membranes of exosomes surround a hydrophilic core, allowing for the simultaneous incorporation of hydrophobic and hydrophilic drugs, nucleic acids, and proteins. Additional capabilities for post-isolation exosome surface modifications with imaging agents, targeting ligands, and covalent linkages also pave the way for their diverse biomedical applications. This review focuses on exosomes: their biogenesis, intracellular trafficking, transportation capacities, and applications with emphasis on the delivery of TNAs and programmable NANPs. We also highlight some of the current challenges and discuss opportunities related to the development of therapeutic exosome-based formulations and their clinical translation.
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Affiliation(s)
- Weina Ke
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, NC 28223, USA
| | - Kirill A Afonin
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, NC 28223, USA.
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39
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Chandler M, Minevich B, Roark B, Viard M, Johnson MB, Rizvi MH, Deaton TA, Kozlov S, Panigaj M, Tracy JB, Yingling YG, Gang O, Afonin KA. Controlled Organization of Inorganic Materials Using Biological Molecules for Activating Therapeutic Functionalities. ACS Appl Mater Interfaces 2021; 13:39030-39041. [PMID: 34402305 PMCID: PMC8654604 DOI: 10.1021/acsami.1c09230] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Precise control over the assembly of biocompatible three-dimensional (3D) nanostructures would allow for programmed interactions within the cellular environment. Nucleic acids can be used as programmable crosslinkers to direct the assembly of quantum dots (QDs) and tuned to demonstrate different interparticle binding strategies. Morphologies of self-assembled QDs are evaluated via gel electrophoresis, transmission electron microscopy, small-angle X-ray scattering, and dissipative particle dynamics simulations, with all results being in good agreement. The controlled assembly of 3D QD organizations is demonstrated in cells via the colocalized emission of multiple assembled QDs, and their immunorecognition is assessed via enzyme-linked immunosorbent assays. RNA interference inducers are also embedded into the interparticle binding strategy to be released in human cells only upon QD assembly, which is demonstrated by specific gene silencing. The programmability and intracellular activity of QD assemblies offer a strategy for nucleic acids to imbue the structure and therapeutic function into the formation of complex networks of nanostructures, while the photoluminescent properties of the material allow for optical tracking in cells in vitro.
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Affiliation(s)
- Morgan Chandler
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, North Carolina 28223, United States
| | - Brian Minevich
- Department of Chemical Engineering, Columbia University, New York, New York 10027, United States
| | - Brandon Roark
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, North Carolina 28223, United States
| | - Mathias Viard
- Laboratory of Integrative Cancer Immunology, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc., Frederick, Maryland 21702, United States
| | - M Brittany Johnson
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, North Carolina 28223, United States
| | - Mehedi H Rizvi
- Department of Materials Science and Engineering, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Thomas A Deaton
- Department of Materials Science and Engineering, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Seraphim Kozlov
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, North Carolina 28223, United States
| | - Martin Panigaj
- Institute of Biology and Ecology, Faculty of Science, Pavol Jozef Safarik University in Kosice, Kosice 04154, Slovak Republic
| | - Joseph B Tracy
- Department of Materials Science and Engineering, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Yaroslava G Yingling
- Department of Materials Science and Engineering, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Oleg Gang
- Department of Chemical Engineering, Columbia University, New York, New York 10027, United States
- Department of Applied Physics and Applied Mathematics, Columbia University, New York, New York 10027, United States
- Center for Functional Nanomaterials, Brookhaven National Laboratory, Upton, New York 11973, USA
| | - Kirill A Afonin
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, North Carolina 28223, United States
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40
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Zhovmer AS, Chandler M, Manning A, Afonin KA, Tabdanov ED. Programmable DNA-augmented hydrogels for controlled activation of human lymphocytes. Nanomedicine 2021; 37:102442. [PMID: 34284132 DOI: 10.1016/j.nano.2021.102442] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Revised: 06/25/2021] [Accepted: 07/07/2021] [Indexed: 12/25/2022]
Abstract
Contractile forces within the planar interface between T cell and antigen-presenting surface mechanically stimulate T cell receptors (TCR) in the mature immune synapses. However, the origin of mechanical stimulation during the initial, i.e., presynaptic, microvilli-based TCR activation in the course of immune surveillance remains unknown and new tools to help address this problem are needed. In this work, we develop nucleic acid nanoassembly (NAN)-based technology for functionalization of hydrogels using isothermal toehold-mediated reassociation of RNA/DNA heteroduplexes. Resulting platform allows for regulation with NAN linkers of 3D force momentum along the TCR mechanical axis, whereas hydrogels contribute to modulation of 2D shear modulus. By utilizing different lengths of NAN linkers conjugated to polyacrylamide gels of different shear moduli, we demonstrate an efficient capture of human T lymphocytes and tunable activation of TCR, as confirmed by T-cell spreading and pY foci.
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Affiliation(s)
- Alexander S Zhovmer
- Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD, USA.
| | - Morgan Chandler
- Department of Chemistry, University of North Carolina at Charlotte, Charlotte, NC, USA
| | - Alexis Manning
- Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD, USA
| | - Kirill A Afonin
- Department of Chemistry, University of North Carolina at Charlotte, Charlotte, NC, USA.
| | - Erdem D Tabdanov
- Department of Pharmacology, Penn State College of Medicine, Hershey, PA, USA.
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41
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Bila D, Radwan Y, Dobrovolskaia MA, Panigaj M, Afonin KA. The Recognition of and Reactions to Nucleic Acid Nanoparticles by Human Immune Cells. Molecules 2021; 26:molecules26144231. [PMID: 34299506 PMCID: PMC8306967 DOI: 10.3390/molecules26144231] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 06/30/2021] [Accepted: 07/08/2021] [Indexed: 11/25/2022] Open
Abstract
The relatively straightforward methods of designing and assembling various functional nucleic acids into nanoparticles offer advantages for applications in diverse diagnostic and therapeutic approaches. However, due to the novelty of this approach, nucleic acid nanoparticles (NANPs) are not yet used in the clinic. The immune recognition of NANPs is among the areas of preclinical investigation aimed at enabling the translation of these novel materials into clinical settings. NANPs’ interactions with the complement system, coagulation systems, and immune cells are essential components of their preclinical safety portfolio. It has been established that NANPs’ physicochemical properties—composition, shape, and size—determine their interactions with immune cells (primarily blood plasmacytoid dendritic cells and monocytes), enable recognition by pattern recognition receptors (PRRs) such as Toll-like receptors (TLRs) and RIG-I-like receptors (RLRs), and mediate the subsequent cytokine response. However, unlike traditional therapeutic nucleic acids (e.g., CpG oligonucleotides), NANPs do not trigger a cytokine response unless they are delivered into the cells using a carrier. Recently, it was discovered that the type of carrier provides an additional tool for regulating both the spectrum and the magnitude of the cytokine response to NANPs. Herein, we review the current knowledge of NANPs’ interactions with various components of the immune system to emphasize the unique properties of these nanomaterials and highlight opportunities for their use in vaccines and immunotherapy.
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Affiliation(s)
- Dominika Bila
- Faculty of Science, Institute of Biology and Ecology, Pavol Jozef Safarik University in Kosice, 04154 Kosice, Slovakia;
| | - Yasmine Radwan
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, NC 28223, USA;
| | - Marina A. Dobrovolskaia
- Nanotechnology Characterization Laboratory, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research Sponsored by the National Cancer Institute, Frederick, MD 21702, USA;
| | - Martin Panigaj
- Faculty of Science, Institute of Biology and Ecology, Pavol Jozef Safarik University in Kosice, 04154 Kosice, Slovakia;
- Correspondence: (M.P.); (K.A.A.); Tel.: +421-55-234-1205 (M.P.); +1-704-687-0685 (K.A.A.)
| | - Kirill A. Afonin
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, NC 28223, USA;
- Correspondence: (M.P.); (K.A.A.); Tel.: +421-55-234-1205 (M.P.); +1-704-687-0685 (K.A.A.)
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42
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Rolband L, Yourston L, Chandler M, Beasock D, Danai L, Kozlov S, Marshall N, Shevchenko O, Krasnoslobodtsev AV, Afonin KA. DNA-Templated Fluorescent Silver Nanoclusters Inhibit Bacterial Growth While Being Non-Toxic to Mammalian Cells. Molecules 2021; 26:4045. [PMID: 34279383 PMCID: PMC8271471 DOI: 10.3390/molecules26134045] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 06/21/2021] [Accepted: 06/29/2021] [Indexed: 11/16/2022] Open
Abstract
Silver has a long history of antibacterial effectiveness. The combination of atomically precise metal nanoclusters with the field of nucleic acid nanotechnology has given rise to DNA-templated silver nanoclusters (DNA-AgNCs) which can be engineered with reproducible and unique fluorescent properties and antibacterial activity. Furthermore, cytosine-rich single-stranded DNA oligonucleotides designed to fold into hairpin structures improve the stability of AgNCs and additionally modulate their antibacterial properties and the quality of observed fluorescent signals. In this work, we characterize the sequence-specific fluorescence and composition of four representative DNA-AgNCs, compare their corresponding antibacterial effectiveness at different pH, and assess cytotoxicity to several mammalian cell lines.
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Affiliation(s)
- Lewis Rolband
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, NC 28223, USA
| | - Liam Yourston
- Department of Physics, University of Nebraska at Omaha, Omaha, NE 68182, USA
| | - Morgan Chandler
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, NC 28223, USA
| | - Damian Beasock
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, NC 28223, USA
| | - Leyla Danai
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, NC 28223, USA
| | - Seraphim Kozlov
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, NC 28223, USA
| | - Nolan Marshall
- Department of Physics, University of Nebraska at Omaha, Omaha, NE 68182, USA
| | - Oleg Shevchenko
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, NC 28223, USA
| | | | - Kirill A Afonin
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, NC 28223, USA
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43
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Affiliation(s)
- Martin Panigaj
- Institute of Biology & Ecology, Faculty of Science, Pavol Jozef Safarik University in Kosice, Kosice, 04154, Slovak Republic
| | - Marina A Dobrovolskaia
- Nanotechnology Characterization Lab, Frederick National Laboratory for Cancer Research sponsored by The National Cancer Institute, Frederick, MD 21702, USA
| | - Kirill A Afonin
- Department of Chemistry, Nanoscale Science Program, University of North Carolina, Charlotte, NC 28223, USA
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44
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Saito RF, Rangel MC, Halman JR, Chandler M, de Sousa Andrade LN, Odete-Bustos S, Furuya TK, Carrasco AGM, Chaves-Filho AB, Yoshinaga MY, Miyamoto S, Afonin KA, Chammas R. Simultaneous silencing of lysophosphatidylcholine acyltransferases 1-4 by nucleic acid nanoparticles (NANPs) improves radiation response of melanoma cells. Nanomedicine 2021; 36:102418. [PMID: 34171470 DOI: 10.1016/j.nano.2021.102418] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2021] [Revised: 05/17/2021] [Accepted: 05/25/2021] [Indexed: 12/19/2022]
Abstract
Radiation induces the generation of platelet-activating factor receptor (PAF-R) ligands, including PAF and oxidized phospholipids. Alternatively, PAF is also synthesized by the biosynthetic enzymes lysophosphatidylcholine acyltransferases (LPCATs) which are expressed by tumor cells including melanoma. The activation of PAF-R by PAF and oxidized lipids triggers a survival response protecting tumor cells from radiation-induced cell death, suggesting the involvement of the PAF/PAF-R axis in radioresistance. Here, we investigated the role of LPCATs in the melanoma cell radiotherapy response. LPCAT is a family of four enzymes, LPCAT1-4, and modular nucleic acid nanoparticles (NANPs) allowed for the simultaneous silencing of all four LPCATs. We found that the in vitro simultaneous silencing of all four LPCAT transcripts by NANPs enhanced the therapeutic effects of radiation in melanoma cells by increasing cell death, reducing long-term cell survival, and activating apoptosis. Thus, we propose that NANPs are an effective strategy for improving radiotherapy efficacy in melanomas.
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Affiliation(s)
- Renata F Saito
- Centro de Investigação Translacional em Oncologia (LIM24), Departamento de Radiologia e Oncologia, Faculdade de Medicina da Universidade de São Paulo and Instituto do Câncer do Estado de São Paulo, São Paulo, SP, Brazil.
| | - Maria Cristina Rangel
- Centro de Investigação Translacional em Oncologia (LIM24), Departamento de Radiologia e Oncologia, Faculdade de Medicina da Universidade de São Paulo and Instituto do Câncer do Estado de São Paulo, São Paulo, SP, Brazil.
| | - Justin R Halman
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, NC, USA.
| | - Morgan Chandler
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, NC, USA.
| | - Luciana Nogueira de Sousa Andrade
- Centro de Investigação Translacional em Oncologia (LIM24), Departamento de Radiologia e Oncologia, Faculdade de Medicina da Universidade de São Paulo and Instituto do Câncer do Estado de São Paulo, São Paulo, SP, Brazil.
| | - Silvina Odete-Bustos
- Centro de Investigação Translacional em Oncologia (LIM24), Departamento de Radiologia e Oncologia, Faculdade de Medicina da Universidade de São Paulo and Instituto do Câncer do Estado de São Paulo, São Paulo, SP, Brazil.
| | - Tatiane Katsue Furuya
- Centro de Investigação Translacional em Oncologia (LIM24), Departamento de Radiologia e Oncologia, Faculdade de Medicina da Universidade de São Paulo and Instituto do Câncer do Estado de São Paulo, São Paulo, SP, Brazil.
| | - Alexis Germán Murillo Carrasco
- Centro de Investigação Translacional em Oncologia (LIM24), Departamento de Radiologia e Oncologia, Faculdade de Medicina da Universidade de São Paulo and Instituto do Câncer do Estado de São Paulo, São Paulo, SP, Brazil.
| | - Adriano B Chaves-Filho
- Laboratório de Lipídeos Modificados, Departamento de Bioquímica, Universidade de São Paulo, São Paulo, Brazil.
| | - Marcos Y Yoshinaga
- Laboratório de Lipídeos Modificados, Departamento de Bioquímica, Universidade de São Paulo, São Paulo, Brazil.
| | - Sayuri Miyamoto
- Laboratório de Lipídeos Modificados, Departamento de Bioquímica, Universidade de São Paulo, São Paulo, Brazil.
| | - Kirill A Afonin
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, NC, USA.
| | - Roger Chammas
- Centro de Investigação Translacional em Oncologia (LIM24), Departamento de Radiologia e Oncologia, Faculdade de Medicina da Universidade de São Paulo and Instituto do Câncer do Estado de São Paulo, São Paulo, SP, Brazil; Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, NC, USA.
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45
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Johnson MB, Chandler M, Afonin KA. Nucleic acid nanoparticles (NANPs) as molecular tools to direct desirable and avoid undesirable immunological effects. Adv Drug Deliv Rev 2021; 173:427-438. [PMID: 33857556 PMCID: PMC8178219 DOI: 10.1016/j.addr.2021.04.011] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Revised: 04/05/2021] [Accepted: 04/08/2021] [Indexed: 12/12/2022]
Abstract
Nucleic acid nanoparticles (NANPs) represent a highly versatile molecular platform for the targeted delivery of various therapeutics. However, despite their promise, further clinical translation of this innovative technology can be hindered by immunological off-target effects. All human cells are equipped with an arsenal of receptors that recognize molecular patterns specific to foreign nucleic acids and understanding the rules that guide this recognition offer the key rationale for the development of therapeutic NANPs with tunable immune stimulation. Numerous recent studies have provided increasing evidence that in addition to NANPs' physicochemical properties and therapeutic effects, their interactions with cells of the immune system can be regulated through multiple independently programmable architectural parameters. The results further suggest that defined immunomodulation by NANPs can either support their immunoquiescent delivery or be used for conditional stimulation of beneficial immunological responses.
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Affiliation(s)
- M Brittany Johnson
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, NC 28223, USA
| | - Morgan Chandler
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, NC 28223, USA
| | - Kirill A Afonin
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, NC 28223, USA.
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46
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Avila YI, Chandler M, Cedrone E, Newton HS, Richardson M, Xu J, Clogston JD, Liptrott NJ, Afonin KA, Dobrovolskaia MA. Induction of Cytokines by Nucleic Acid Nanoparticles (NANPs) Depends on the Type of Delivery Carrier. Molecules 2021; 26:652. [PMID: 33513786 PMCID: PMC7865455 DOI: 10.3390/molecules26030652] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 01/20/2021] [Accepted: 01/21/2021] [Indexed: 12/12/2022] Open
Abstract
Recent insights into the immunostimulatory properties of nucleic acid nanoparticles (NANPs) have demonstrated that variations in the shape, size, and composition lead to distinct patterns in their immunostimulatory properties. While most of these studies have used a single lipid-based carrier to allow for NANPs' intracellular delivery, it is now apparent that the platform for delivery, which has historically been a hurdle for therapeutic nucleic acids, is an additional means to tailoring NANP immunorecognition. Here, the use of dendrimers for the delivery of NANPs is compared to the lipid-based platform and the differences in resulting cytokine induction are presented.
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Affiliation(s)
- Yelixza I. Avila
- Nanoscale Science Program, Department of Chemistry, University of North Carolina Charlotte, Charlotte, NC 28223-0001, USA; (Y.I.A.); (M.C.); (M.R.)
| | - Morgan Chandler
- Nanoscale Science Program, Department of Chemistry, University of North Carolina Charlotte, Charlotte, NC 28223-0001, USA; (Y.I.A.); (M.C.); (M.R.)
| | - Edward Cedrone
- Nanotechnology Characterization Laboratory, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research Sponsored by the National Cancer Institute, Frederick, MD 21702, USA; (E.C.); (H.S.N.); (J.X.); (J.D.C.)
| | - Hannah S. Newton
- Nanotechnology Characterization Laboratory, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research Sponsored by the National Cancer Institute, Frederick, MD 21702, USA; (E.C.); (H.S.N.); (J.X.); (J.D.C.)
| | - Melina Richardson
- Nanoscale Science Program, Department of Chemistry, University of North Carolina Charlotte, Charlotte, NC 28223-0001, USA; (Y.I.A.); (M.C.); (M.R.)
| | - Jie Xu
- Nanotechnology Characterization Laboratory, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research Sponsored by the National Cancer Institute, Frederick, MD 21702, USA; (E.C.); (H.S.N.); (J.X.); (J.D.C.)
| | - Jeffrey D. Clogston
- Nanotechnology Characterization Laboratory, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research Sponsored by the National Cancer Institute, Frederick, MD 21702, USA; (E.C.); (H.S.N.); (J.X.); (J.D.C.)
| | - Neill J. Liptrott
- Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L7 3NY, UK;
| | - Kirill A. Afonin
- Nanoscale Science Program, Department of Chemistry, University of North Carolina Charlotte, Charlotte, NC 28223-0001, USA; (Y.I.A.); (M.C.); (M.R.)
| | - Marina A. Dobrovolskaia
- Nanotechnology Characterization Laboratory, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research Sponsored by the National Cancer Institute, Frederick, MD 21702, USA; (E.C.); (H.S.N.); (J.X.); (J.D.C.)
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47
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Johnson MB, Halman JR, Miller DK, Cooper JS, Khisamutdinov E, Marriott I, Afonin KA. The immunorecognition, subcellular compartmentalization, and physicochemical properties of nucleic acid nanoparticles can be controlled by composition modification. Nucleic Acids Res 2020; 48:11785-11798. [PMID: 33091133 PMCID: PMC7672449 DOI: 10.1093/nar/gkaa908] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Revised: 09/24/2020] [Accepted: 10/01/2020] [Indexed: 12/18/2022] Open
Abstract
Nucleic acid nanoparticles (NANPs) have become powerful new platforms as therapeutic and diagnostic tools due to the innate biological ability of nucleic acids to identify target molecules or silence genes involved in disease pathways. However, the clinical application of NANPs has been limited by factors such as chemical instability, inefficient intracellular delivery, and the triggering of detrimental inflammatory responses following innate immune recognition of nucleic acids. Here, we have studied the effects of altering the chemical composition of a circumscribed panel of NANPs that share the same connectivity, shape, size, charge and sequences. We show that replacing RNA strands with either DNA or chemical analogs increases the enzymatic and thermodynamic stability of NANPs. Furthermore, we have found that such composition changes affect delivery efficiency and determine subcellular localization, effects that could permit the targeted delivery of NANP-based therapeutics and diagnostics. Importantly, we have determined that altering NANP composition can dictate the degree and mechanisms by which cell immune responses are initiated. While RNA NANPs trigger both TLR7 and RIG-I mediated cytokine and interferon production, DNA NANPs stimulate minimal immune activation. Importantly, incorporation of 2'F modifications abrogates RNA NANP activation of TLR7 but permits RIG-I dependent immune responses. Furthermore, 2'F modifications of DNA NANPs significantly enhances RIG-I mediated production of both proinflammatory cytokines and interferons. Collectively this indicates that off-target effects may be reduced and/or desirable immune responses evoked based upon NANPs modifications. Together, our studies show that NANP composition provides a simple way of controlling the immunostimulatory potential, and physicochemical and delivery characteristics, of such platforms.
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Affiliation(s)
- Morgan Brittany Johnson
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, NC, USA
| | - Justin R Halman
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, NC 28223, USA
| | - Daniel K Miller
- Department of Chemistry, Ball State University, Muncie, IN 47306, USA
| | - Joseph S Cooper
- Department of Chemistry, Ball State University, Muncie, IN 47306, USA
| | | | - Ian Marriott
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, NC, USA
| | - Kirill A Afonin
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, NC 28223, USA
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48
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Nordmeier S, Ke W, Afonin KA, Portnoy V. Exosome mediated delivery of functional nucleic acid nanoparticles (NANPs). Nanomedicine 2020; 30:102285. [PMID: 32781137 PMCID: PMC7680442 DOI: 10.1016/j.nano.2020.102285] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2020] [Revised: 07/25/2020] [Accepted: 07/30/2020] [Indexed: 12/14/2022]
Abstract
RNAi-based technologies have shown biomedical potential; however, safe and efficient delivery of RNA remains a barrier for their broader clinical applications. Nucleic acid nanoparticles (NANPs) programmed to self-assemble and organize multiple therapeutic nucleic acids (TNAs) also became attractive candidates for diverse therapeutic options. Various synthetic nanocarriers are used to deliver TNAs and NANPs, but their clinical translation is limited due to immunotoxicity. Exosomes are cell-derived nanovesicles involved in cellular communication. Due to their ability to deliver biomolecules, exosomes are a novel delivery choice. In this study, we explored the exosome-mediated delivery of NANPs designed to target GFP. We assessed the intracellular uptake, gene silencing efficiency, and immunostimulation of exosomes loaded with NANPs. We also confirmed that interdependent RNA/DNA fibers upon recognition of each other after delivery, can conditionally activate NF-kB decoys and prevent pro-inflammatory cytokines. Our study overcomes challenges in TNA delivery and demonstrates future studies in drug delivery systems.
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Affiliation(s)
| | - Weina Ke
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, NC, USA
| | - Kirill A Afonin
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, NC, USA.
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Afonin KA, Dobrovolskaia MA, Church G, Bathe M. Opportunities, Barriers, and a Strategy for Overcoming Translational Challenges to Therapeutic Nucleic Acid Nanotechnology. ACS Nano 2020; 14:9221-9227. [PMID: 32706238 PMCID: PMC7731581 DOI: 10.1021/acsnano.0c04753] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Recent clinical successes using therapeutic nucleic acids (TNAs) have accelerated the transition of nucleic acid nanotechnology toward therapeutic applications. Significant progress in the development, production, and characterization of nucleic acid nanomaterials and nucleic acid nanoparticles (NANPs), as well as abundant proof-of-concept data, are paving the way toward biomedical applications of these materials. This recent progress has catalyzed the development of new strategies for biosensing, imaging, drug delivery, and immunotherapies with previously unrecognized opportunities and identified some barriers that may impede the broader clinical translation of NANP technologies. A recent workshop sponsored by the Kavli Foundation and the Materials Research Society discussed the future directions and current challenges for the development of therapeutic nucleic acid nanotechnology. Herein, we communicate discussions on the opportunities, barriers, and strategies for realizing the clinical grand challenge of TNA nanotechnology, with a focus on ways to overcome barriers to advance NANPs to the clinic.
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Affiliation(s)
- Kirill A Afonin
- Nanoscale Science Program, Department of Chemistry, The University of North Carolina at Charlotte, Charlotte, North Carolina 28223, United States
| | - Marina A Dobrovolskaia
- Nanotechnology Characterization Lab, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research sponsored by the National Cancer Institute, Frederick, Maryland 21702, United States
| | - George Church
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, United States
- Wyss Institute for Biologically Inspired Engineering, Boston, Massachusetts 02115, United States
- Harvard Graduate Program in Biological and Biomedical Sciences, Boston, Massachusetts 02115, United States
| | - Mark Bathe
- Department of Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
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Yourston L, Rolband L, West C, Lushnikov A, Afonin KA, Krasnoslobodtsev AV. Tuning properties of silver nanoclusters with RNA nanoring assemblies. Nanoscale 2020; 12:16189-16200. [PMID: 32705105 DOI: 10.1039/d0nr03589k] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Combining atomically resolved DNA-templated silver nanoclusters (AgNCs) with nucleic acid nanotechnology opens new exciting possibilities for engineering bioinorganic nanomaterials with uniquely tunable properties. In this unforeseen cooperation, nucleic acids not only drive the formation of AgNCs but also promote their spatial organization in supra-assemblies. In this work, we confirm the feasibility of this approach using programmable RNA rings to control formation and optical properteis of six individual AgNCs. "Red" (λEXC/λEM = 565/623 nm) and "green" (λEXC/λEM = 440/523 nm) emitting AgNCs are templated on cytosine-rich DNA fragments embedded into the RNA rings. Optical properties of the AgNCs formed on the RNA rings are characterized in detail. While all "red" species passively transition to "green" emitters with time, the initial fluorescent properties and relative stabilities of "red" AgNCs can be regulated by altering the relative orientation of AgNCs within the RNA rings. As such, the oxidative stability increases dramatically for AgNC positioned towards the center of the RNA rings rather than facing outward. Overall, our findings expand the existing AgNC fluorescent toolkit while uncovering the complexity of the AgNC electronic structures with the abundance of possibilities for controlling de-excitation processes.
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Affiliation(s)
- Liam Yourston
- Department of Physics, University of Nebraska Omaha, Omaha, NE 68182, USA.
| | - Lewis Rolband
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, NC 28223, USA
| | - Caroline West
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, NC 28223, USA
| | - Alexander Lushnikov
- Nanoimaging Core Facility at the University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Kirill A Afonin
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, NC 28223, USA
| | - Alexey V Krasnoslobodtsev
- Department of Physics, University of Nebraska Omaha, Omaha, NE 68182, USA. and Nanoimaging Core Facility at the University of Nebraska Medical Center, Omaha, NE 68198, USA
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